rs509423

Variant names:

• chr4-115140173-T-A
• rs509423

Your query was ambiguous. Multiple possible variants found:

• chr4-115140173-T-A
• chr4-115140173-T-G

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 0.746 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.805 AC: 33434 AN: 41518

American (AMR) AF: 0.712 AC: 10876 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1853 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3783 AN: 5166

South Asian (SAS) AF: 0.571 AC: 2751 AN: 4818

European-Finnish (FIN) AF: 0.812 AC: 8612 AN: 10606

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49773 AN: 67990

Other (OTH) AF: 0.718 AC: 1518 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs509423; hg19: chr4-116061329;