dbSNP rs841603: LOC124902904:n.27158549G>A (chr12-27158549-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.491 in 151,946 control chromosomes in the GnomAD database, including 19,496 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 0.49 ( 19496 hom., cov: 32)

Consequence

LOC124902904
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

Publications

5 publications found

Variant links:

Genes affected

LOC124902904 (HGNC:):

LOC124902904 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902904		n.27158549G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000256226	ENST00000538920.1 link	n.243+2602C>T	intron_variant	Intron 1 of 1	5
ENSG00000256226	ENST00000540595.2 link	n.310+2602C>T	intron_variant	Intron 2 of 2	5
ENSG00000256226	ENST00000824827.1 link	n.280+2602C>T	intron_variant	Intron 2 of 2
ENSG00000256226	ENST00000824828.1 link	n.71+123C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74612

AN:

151828

Hom.:

19496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.407

Gnomad AMI

AF:

0.494

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.595

Gnomad OTH

AF:

0.496

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

GnomAD4 genome

AF:

0.491

AC:

74634

AN:

151946

Hom.:

19496

Cov.:

AF XY:

0.484

AC XY:

35925

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.407

AC:

16853

AN:

41442

American (AMR)

AF:

0.378

AC:

5772

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1540

AN:

3472

East Asian (EAS)

AF:

0.132

AC:

681

AN:

5166

South Asian (SAS)

AF:

0.364

AC:

1751

AN:

4816

European-Finnish (FIN)

AF:

0.570

AC:

6001

AN:

10524

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.595

AC:

40437

AN:

67956

Other (OTH)

AF:

0.494

AC:

1041

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1837

3675

5512

7350

9187

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.529

Hom.:

9429

Bravo

AF:

0.470

Asia WGS

AF:

0.274

AC:

955

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

1.3

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