rs4864976

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 0.221 in 152,016 control chromosomes in the GnomAD database, including 4,992 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 0.22 ( 4992 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.256
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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:
0.221
AC:
33545
AN:
151898
Hom.:
4976
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.422
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.186
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.271
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.128
Gnomad OTH
AF:
0.218
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.221
AC:
33597
AN:
152016
Hom.:
4992
Cov.:
32
AF XY:
0.219
AC XY:
16258
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.422
Gnomad4 AMR
AF:
0.186
Gnomad4 ASJ
AF:
0.131
Gnomad4 EAS
AF:
0.271
Gnomad4 SAS
AF:
0.134
Gnomad4 FIN
AF:
0.134
Gnomad4 NFE
AF:
0.128
Gnomad4 OTH
AF:
0.216
Alfa
AF:
0.144
Hom.:
3718
Bravo
AF:
0.238
Asia WGS
AF:
0.212
AC:
741
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.1
DANN
Benign
0.32

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: rs4864976; hg19: chr4-56153732; API