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GeneBe

rs4648308

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 0.262 in 152,046 control chromosomes in the GnomAD database, including 7,883 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 ( 7883 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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:
0.262
AC:
39810
AN:
151928
Hom.:
7840
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.555
Gnomad AMI
AF:
0.0779
Gnomad AMR
AF:
0.196
Gnomad ASJ
AF:
0.232
Gnomad EAS
AF:
0.0483
Gnomad SAS
AF:
0.193
Gnomad FIN
AF:
0.0821
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.152
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.262
AC:
39911
AN:
152046
Hom.:
7883
Cov.:
32
AF XY:
0.255
AC XY:
18977
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.556
Gnomad4 AMR
AF:
0.197
Gnomad4 ASJ
AF:
0.232
Gnomad4 EAS
AF:
0.0481
Gnomad4 SAS
AF:
0.193
Gnomad4 FIN
AF:
0.0821
Gnomad4 NFE
AF:
0.152
Gnomad4 OTH
AF:
0.259
Alfa
AF:
0.225
Hom.:
886
Bravo
AF:
0.283
Asia WGS
AF:
0.186
AC:
646
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.12
DANN
Benign
0.15

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: rs4648308; hg19: chr1-186640617; API