rs1374313

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.551 in 152,094 control chromosomes in the GnomAD database, including 24,281 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 0.55 ( 24281 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.06
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.551
AC:
83773
AN:
151976
Hom.:
24234
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.743
Gnomad AMI
AF:
0.564
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.496
Gnomad EAS
AF:
0.379
Gnomad SAS
AF:
0.386
Gnomad FIN
AF:
0.514
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.496
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.551
AC:
83873
AN:
152094
Hom.:
24281
Cov.:
33
AF XY:
0.547
AC XY:
40630
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.744
Gnomad4 AMR
AF:
0.429
Gnomad4 ASJ
AF:
0.496
Gnomad4 EAS
AF:
0.378
Gnomad4 SAS
AF:
0.386
Gnomad4 FIN
AF:
0.514
Gnomad4 NFE
AF:
0.496
Gnomad4 OTH
AF:
0.523
Alfa
AF:
0.499
Hom.:
31799
Bravo
AF:
0.554
Asia WGS
AF:
0.410
AC:
1423
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
0.25
DANN
Benign
0.29

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1374313; hg19: chr2-120145655; API