rs4638547

Positions:

• chr15-73042652-C-T

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 0.552 in 151,864 control chromosomes in the GnomAD database, including 23,871 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 0.55 (23871 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83781 AN: 151746 Hom.: 23855 Cov.: 30

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.552 AC: 83840 AN: 151864 Hom.: 23871 Cov.: 30 AF XY: 0.546 AC XY: 40542 AN XY: 74218

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.574

Alfa AF: 0.605 Hom.: 44689

Bravo AF: 0.549

Asia WGS AF: 0.389 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4638547; hg19: chr15-73334993;