chr7-126256694-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0176 in 152,056 control chromosomes in the GnomAD database, including 39 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 0.018 ( 39 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.707
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=-1.01).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0176 (2677/152056) while in subpopulation NFE AF= 0.0257 (1746/67968). AF 95% confidence interval is 0.0247. There are 39 homozygotes in gnomad4. There are 1299 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 39 gene

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:
0.0176
AC:
2676
AN:
151938
Hom.:
39
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00329
Gnomad AMI
AF:
0.0617
Gnomad AMR
AF:
0.0115
Gnomad ASJ
AF:
0.0190
Gnomad EAS
AF:
0.000387
Gnomad SAS
AF:
0.00477
Gnomad FIN
AF:
0.0406
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0257
Gnomad OTH
AF:
0.0182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0176
AC:
2677
AN:
152056
Hom.:
39
Cov.:
32
AF XY:
0.0175
AC XY:
1299
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.00328
Gnomad4 AMR
AF:
0.0115
Gnomad4 ASJ
AF:
0.0190
Gnomad4 EAS
AF:
0.000388
Gnomad4 SAS
AF:
0.00477
Gnomad4 FIN
AF:
0.0406
Gnomad4 NFE
AF:
0.0257
Gnomad4 OTH
AF:
0.0180
Alfa
AF:
0.0166
Hom.:
7
Bravo
AF:
0.0139
Asia WGS
AF:
0.00318
AC:
12
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.77
DANN
Benign
0.31

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: rs117982730; hg19: chr7-125896748; API