rs531460

chr4-46208253-A-G

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 0.636 in 151,786 control chromosomes in the GnomAD database, including 31,405 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 (31405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 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: 0.636 AC: 96468 AN: 151668 Hom.: 31361 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.636 AC: 96558 AN: 151786 Hom.: 31405 Cov.: 32 AF XY: 0.636 AC XY: 47170 AN XY: 74138

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.638

Alfa AF: 0.600 Hom.: 3485

Bravo AF: 0.632

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.0080
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531460; hg19: chr4-46210270;