rs7662694

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 0.254 in 152,012 control chromosomes in the GnomAD database, including 5,168 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 0.25 ( 5168 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.311
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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:
0.254
AC:
38538
AN:
151894
Hom.:
5160
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.223
Gnomad AMI
AF:
0.521
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.289
Gnomad EAS
AF:
0.434
Gnomad SAS
AF:
0.230
Gnomad FIN
AF:
0.303
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.248
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38574
AN:
152012
Hom.:
5168
Cov.:
32
AF XY:
0.260
AC XY:
19313
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.223
Gnomad4 AMR
AF:
0.356
Gnomad4 ASJ
AF:
0.289
Gnomad4 EAS
AF:
0.435
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.303
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.250
Alfa
AF:
0.239
Hom.:
925
Bravo
AF:
0.262
Asia WGS
AF:
0.336
AC:
1164
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
7.1
DANN
Benign
0.80

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: rs7662694; hg19: chr4-11120760; API