rs6902875

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 0.436 in 152,056 control chromosomes in the GnomAD database, including 18,987 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 0.44 ( 18987 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.436
AC:
66184
AN:
151938
Hom.:
18934
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.819
Gnomad AMI
AF:
0.181
Gnomad AMR
AF:
0.290
Gnomad ASJ
AF:
0.258
Gnomad EAS
AF:
0.300
Gnomad SAS
AF:
0.344
Gnomad FIN
AF:
0.290
Gnomad MID
AF:
0.335
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.386
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2
Hom.:
0
AC XY:
0
AN XY:
0
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.436
AC:
66286
AN:
152056
Hom.:
18987
Cov.:
32
AF XY:
0.429
AC XY:
31892
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.819
Gnomad4 AMR
AF:
0.290
Gnomad4 ASJ
AF:
0.258
Gnomad4 EAS
AF:
0.299
Gnomad4 SAS
AF:
0.342
Gnomad4 FIN
AF:
0.290
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.391
Alfa
AF:
0.308
Hom.:
10641
Bravo
AF:
0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.8
DANN
Benign
0.58

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: rs6902875; hg19: chr6-132617072; COSMIC: COSV60948306; API