rs4331968

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 0.291 in 152,182 control chromosomes in the GnomAD database, including 7,035 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 0.29 ( 7035 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.329
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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44282
AN:
152064
Hom.:
7009
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.422
Gnomad AMI
AF:
0.129
Gnomad AMR
AF:
0.239
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.170
Gnomad SAS
AF:
0.325
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.243
Gnomad OTH
AF:
0.314
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.291
AC:
44354
AN:
152182
Hom.:
7035
Cov.:
33
AF XY:
0.287
AC XY:
21341
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.422
Gnomad4 AMR
AF:
0.238
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.171
Gnomad4 SAS
AF:
0.325
Gnomad4 FIN
AF:
0.192
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.321
Alfa
AF:
0.268
Hom.:
703
Bravo
AF:
0.296
Asia WGS
AF:
0.295
AC:
1026
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.2
DANN
Benign
0.84

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: rs4331968; hg19: chr6-36623243; API