dbSNP rs1411374: LOC124902135:c.80+2181T>A (chr9-27713846-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XM_047424284.1(LOC124902135):c.80+2181T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,168 control chromosomes in the GnomAD database, including 3,135 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 0.19 ( 3135 hom., cov: 32)

Consequence

LOC124902135
XM_047424284.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839

Publications

2 publications found

Variant links:

Genes affected

LOC124902135 (HGNC:):

LOC124902135 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902135	XM_047424284.1 link	c.80+2181T>A		intron_variant	Intron 1 of 2		XP_047280240.1
LOC124902135	XR_007061442.1 link	n.139+2181T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28895

AN:

152048

Hom.:

3131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.0503

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.200

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.190

AC:

28907

AN:

152168

Hom.:

3135

Cov.:

AF XY:

0.194

AC XY:

14450

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.112

AC:

4651

AN:

41512

American (AMR)

AF:

0.297

AC:

4537

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

791

AN:

3472

East Asian (EAS)

AF:

0.0504

AC:

261

AN:

5178

South Asian (SAS)

AF:

0.275

AC:

1330

AN:

4830

European-Finnish (FIN)

AF:

0.198

AC:

2094

AN:

10590

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.214

AC:

14563

AN:

67982

Other (OTH)

AF:

0.197

AC:

415

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1196

2392

3589

4785

5981

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.199

Hom.:

402

Bravo

AF:

0.194

Asia WGS

AF:

0.164

AC:

569

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.81

(source)

DANN

Benign

0.71

PhyloP100

-0.84

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over