5-147964808-A-G

Variant names:

• chr5-147964808-A-G
• rs1363530

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 0.811 in 152,078 control chromosomes in the GnomAD database, including 50,822 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 0.81 (50822 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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: 0.811 AC: 123220 AN: 151960 Hom.: 50752 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.811 AC: 123349 AN: 152078 Hom.: 50822 Cov.: 31 AF XY: 0.815 AC XY: 60572 AN XY: 74330

African (AFR) AF: 0.953 AC: 39569 AN: 41512

American (AMR) AF: 0.839 AC: 12804 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2605 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4742 AN: 5168

South Asian (SAS) AF: 0.824 AC: 3971 AN: 4820

European-Finnish (FIN) AF: 0.771 AC: 8137 AN: 10556

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48988 AN: 67968

Other (OTH) AF: 0.791 AC: 1668 AN: 2110

Alfa AF: 0.767 Hom.: 7652

Bravo AF: 0.823

Asia WGS AF: 0.887 AC: 3085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1363530; hg19: chr5-147344371;