rs782895

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 0.279 in 151,950 control chromosomes in the GnomAD database, including 6,217 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 0.28 ( 6217 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.321
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=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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:
0.279
AC:
42319
AN:
151834
Hom.:
6205
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.378
Gnomad AMI
AF:
0.231
Gnomad AMR
AF:
0.240
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.149
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.172
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.259
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.279
AC:
42370
AN:
151950
Hom.:
6217
Cov.:
32
AF XY:
0.275
AC XY:
20389
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.378
Gnomad4 AMR
AF:
0.240
Gnomad4 ASJ
AF:
0.252
Gnomad4 EAS
AF:
0.149
Gnomad4 SAS
AF:
0.225
Gnomad4 FIN
AF:
0.172
Gnomad4 NFE
AF:
0.259
Gnomad4 OTH
AF:
0.272
Alfa
AF:
0.254
Hom.:
632
Bravo
AF:
0.283
Asia WGS
AF:
0.200
AC:
694
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.59

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: rs782895; hg19: chr7-84530326; API