chr6-40697676-C-T

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 0.264 in 152,108 control chromosomes in the GnomAD database, including 5,997 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 0.26 ( 5997 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.951
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=-0.74).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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:
0.264
AC:
40110
AN:
151990
Hom.:
5984
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.403
Gnomad AMI
AF:
0.136
Gnomad AMR
AF:
0.248
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.295
Gnomad SAS
AF:
0.399
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.192
Gnomad OTH
AF:
0.280
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
40138
AN:
152108
Hom.:
5997
Cov.:
33
AF XY:
0.265
AC XY:
19700
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.403
Gnomad4 AMR
AF:
0.248
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.295
Gnomad4 SAS
AF:
0.398
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.192
Gnomad4 OTH
AF:
0.279
Alfa
AF:
0.209
Hom.:
6396
Bravo
AF:
0.272
Asia WGS
AF:
0.356
AC:
1242
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
11
DANN
Benign
0.77

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: rs6931798; hg19: chr6-40665415; API