rs1504497

chr4-45946427-G-A

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 0.641 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.613

Alfa AF: 0.586 Hom.: 12296

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504497; hg19: chr4-45948444;