Genetic Variant ASIC1:c.1205+202T>C (chr12-50080257-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001095.4(ASIC1):c.1205+202T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 782,568 control chromosomes in the GnomAD database, including 177,762 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36350 hom., cov: 32)

Exomes 𝑓: 0.67 ( 141412 hom. )

Consequence

ASIC1
NM_001095.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

14 publications found

Variant links:

Genes affected

ASIC1 (HGNC:100): (acid sensing ion channel subunit 1) This gene encodes a member of the acid-sensing ion channel (ASIC) family of proteins, which are part of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily. Members of the ASIC family are sensitive to amiloride and function in neurotransmission. The encoded proteins function in learning, pain transduction, touch sensation, and development of memory and fear. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2012]

ASIC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASIC1	NM_001095.4 link	c.1205+202T>C		intron_variant	Intron 8 of 11	ENST00000447966.7	NP_001086.2	P78348-2A8K1U5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASIC1	ENST00000447966.7 link	c.1205+202T>C		intron_variant	Intron 8 of 11	1	NM_001095.4	ENSP00000400228.3		P78348-2

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104607

AN:

151940

Hom.:

36293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.728

Gnomad AMI

AF:

0.722

Gnomad AMR

AF:

0.733

Gnomad ASJ

AF:

0.795

Gnomad EAS

AF:

0.850

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.639

Gnomad OTH

AF:

0.699

GnomAD4 exome

AF:

0.665

AC:

419557

AN:

630510

Hom.:

141412

AF XY:

0.662

AC XY:

217416

AN XY:

328532

show subpopulations

African (AFR)

AF:

0.730

AC:

11350

AN:

15542

American (AMR)

AF:

0.732

AC:

14448

AN:

19750

Ashkenazi Jewish (ASJ)

AF:

0.801

AC:

12589

AN:

15708

East Asian (EAS)

AF:

0.874

AC:

28247

AN:

32330

South Asian (SAS)

AF:

0.607

AC:

30374

AN:

50060

European-Finnish (FIN)

AF:

0.689

AC:

22187

AN:

32198

Middle Eastern (MID)

AF:

0.712

AC:

1751

AN:

2460

European-Non Finnish (NFE)

AF:

0.643

AC:

276654

AN:

430226

Other (OTH)

AF:

0.681

AC:

21957

AN:

32236

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

7386

14772

22157

29543

36929

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4116

8232

12348

16464

20580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.689

AC:

104727

AN:

152058

Hom.:

36350

Cov.:

AF XY:

0.695

AC XY:

51661

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.729

AC:

30214

AN:

41454

American (AMR)

AF:

0.733

AC:

11201

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.795

AC:

2761

AN:

3472

East Asian (EAS)

AF:

0.850

AC:

4392

AN:

5168

South Asian (SAS)

AF:

0.600

AC:

2894

AN:

4820

European-Finnish (FIN)

AF:

0.710

AC:

7514

AN:

10586

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.639

AC:

43423

AN:

67972

Other (OTH)

AF:

0.698

AC:

1469

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1683

3367

5050

6734

8417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.663

Hom.:

133415

Bravo

AF:

0.695

Asia WGS

AF:

0.710

AC:

2466

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

(source)

DANN

Benign

0.58

PhyloP100

-1.4

PromoterAI

0.0062

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over