rs4638547

Variant names:

• chr15-73042652-C-T
• rs4638547

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 0.552 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.552 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

African (AFR) AF: 0.479 AC: 19846 AN: 41394

American (AMR) AF: 0.564 AC: 8598 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2167 AN: 3468

East Asian (EAS) AF: 0.164 AC: 847 AN: 5156

South Asian (SAS) AF: 0.577 AC: 2776 AN: 4814

European-Finnish (FIN) AF: 0.525 AC: 5517 AN: 10514

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42081 AN: 67956

Other (OTH) AF: 0.574 AC: 1212 AN: 2112

Alfa AF: 0.596 Hom.: 97926

Bravo AF: 0.549

Asia WGS AF: 0.389 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4638547; hg19: chr15-73334993;