rs6937034

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 0.0479 in 152,284 control chromosomes in the GnomAD database, including 587 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 0.048 ( 587 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.418
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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:
0.0477
AC:
7265
AN:
152166
Hom.:
576
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0448
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.0336
Gnomad ASJ
AF:
0.0383
Gnomad EAS
AF:
0.417
Gnomad SAS
AF:
0.0308
Gnomad FIN
AF:
0.0281
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0298
Gnomad OTH
AF:
0.0492
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0479
AC:
7287
AN:
152284
Hom.:
587
Cov.:
32
AF XY:
0.0487
AC XY:
3629
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0447
Gnomad4 AMR
AF:
0.0336
Gnomad4 ASJ
AF:
0.0383
Gnomad4 EAS
AF:
0.418
Gnomad4 SAS
AF:
0.0305
Gnomad4 FIN
AF:
0.0281
Gnomad4 NFE
AF:
0.0298
Gnomad4 OTH
AF:
0.0591
Alfa
AF:
0.0433
Hom.:
803
Bravo
AF:
0.0501
Asia WGS
AF:
0.141
AC:
488
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.4
DANN
Benign
0.54

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: rs6937034; hg19: chr6-33079766; API