15-48407732-T-C

Variant names:

• chr15-48407732-T-C
• rs2114438

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 0.59 in 151,616 control chromosomes in the GnomAD database, including 27,969 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 0.59 (27969 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 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: 0.590 AC: 89430 AN: 151506 Hom.: 27975 Cov.: 34

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.590 AC: 89437 AN: 151616 Hom.: 27969 Cov.: 34 AF XY: 0.590 AC XY: 43733 AN XY: 74080

African (AFR) AF: 0.363 AC: 15045 AN: 41486

American (AMR) AF: 0.629 AC: 9572 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2628 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2066 AN: 4746

South Asian (SAS) AF: 0.663 AC: 3189 AN: 4810

European-Finnish (FIN) AF: 0.672 AC: 7103 AN: 10576

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47868 AN: 67994

Other (OTH) AF: 0.604 AC: 1276 AN: 2112

Alfa AF: 0.653 Hom.: 11993

Bravo AF: 0.574

Asia WGS AF: 0.478 AC: 1658 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2114438; hg19: chr15-48699929;