5-147964808-A-G

Variant names:

• chr5-147964808-A-G
• rs1363530

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.791

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363530; hg19: chr5-147344371;