rs1504497

Variant names:

• chr4-45946427-G-A
• rs1504497

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 0.641 in 152,074 control chromosomes in the GnomAD database, including 32,711 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 0.64 (32711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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: 0.640 AC: 97321 AN: 151956 Hom.: 32651 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.641 AC: 97451 AN: 152074 Hom.: 32711 Cov.: 32 AF XY: 0.636 AC XY: 47268 AN XY: 74346

African (AFR) AF: 0.839 AC: 34828 AN: 41492

American (AMR) AF: 0.570 AC: 8704 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1674 AN: 5158

South Asian (SAS) AF: 0.410 AC: 1980 AN: 4830

European-Finnish (FIN) AF: 0.638 AC: 6749 AN: 10572

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39539 AN: 67972

Other (OTH) AF: 0.613 AC: 1293 AN: 2108

Alfa AF: 0.588 Hom.: 16959

Bravo AF: 0.647

Asia WGS AF: 0.390 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.52
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs1504497; hg19: chr4-45948444;