rs509423

chr4-115140173-T-Achr4-115140173-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 0.746 in 152,168 control chromosomes in the GnomAD database, including 42,744 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 0.75 (42744 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.746 AC: 113495 AN: 152052 Hom.: 42699 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.746 AC: 113590 AN: 152168 Hom.: 42744 Cov.: 33 AF XY: 0.745 AC XY: 55466 AN XY: 74410

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.718

Alfa AF: 0.737 Hom.: 5125

Bravo AF: 0.750

Asia WGS AF: 0.656 AC: 2280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs509423; hg19: chr4-116061329;