15-43724219-T-C

Variant names:

• chr15-43724219-T-C
• rs10438303

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 0.161 in 152,168 control chromosomes in the GnomAD database, including 2,596 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 0.16 (2596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24470 AN: 152050 Hom.: 2589 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.161 AC: 24514 AN: 152168 Hom.: 2596 Cov.: 32 AF XY: 0.159 AC XY: 11847 AN XY: 74432

African (AFR) AF: 0.288 AC: 11953 AN: 41492

American (AMR) AF: 0.178 AC: 2718 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1420 AN: 5180

South Asian (SAS) AF: 0.142 AC: 685 AN: 4828

European-Finnish (FIN) AF: 0.0403 AC: 428 AN: 10608

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6222 AN: 67988

Other (OTH) AF: 0.156 AC: 329 AN: 2112

Alfa AF: 0.126 Hom.: 4302

Bravo AF: 0.180

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs10438303; hg19: chr15-44016417;