5-56808481-A-G

Variant names:

• chr5-56808481-A-G
• rs10461617

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.754 in 149,348 control chromosomes in the GnomAD database, including 42,427 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 0.75 (42427 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.754 AC: 112471 AN: 149238 Hom.: 42398 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.754

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.754 AC: 112546 AN: 149348 Hom.: 42427 Cov.: 31 AF XY: 0.749 AC XY: 54773 AN XY: 73094

African (AFR) AF: 0.671 AC: 26143 AN: 38944

American (AMR) AF: 0.670 AC: 10167 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2831 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2995 AN: 5162

South Asian (SAS) AF: 0.771 AC: 3710 AN: 4810

European-Finnish (FIN) AF: 0.809 AC: 8534 AN: 10548

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55734 AN: 67948

Other (OTH) AF: 0.756 AC: 1575 AN: 2084

Alfa AF: 0.779 Hom.: 106189

Bravo AF: 0.724

Asia WGS AF: 0.690 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10461617; hg19: chr5-56104308;