rs1905262

chr4-155581296-T-Achr4-155581296-T-Cchr4-155581296-T-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 0.505 in 152,014 control chromosomes in the GnomAD database, including 19,767 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 0.51 (19767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.505 AC: 76773 AN: 151896 Hom.: 19761 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.505 AC: 76827 AN: 152014 Hom.: 19767 Cov.: 32 AF XY: 0.515 AC XY: 38268 AN XY: 74296

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.499

Alfa AF: 0.380 Hom.: 1038

Bravo AF: 0.493

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.5
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1905262; hg19: chr4-156502448;