15-74804102-T-C

Variant names:

• chr15-74804102-T-C
• rs1378938

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 0.64 in 152,082 control chromosomes in the GnomAD database, including 31,702 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 0.64 (31702 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 36 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 (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.640 AC: 97286 AN: 151964 Hom.: 31699 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.640 AC: 97331 AN: 152082 Hom.: 31702 Cov.: 33 AF XY: 0.635 AC XY: 47209 AN XY: 74370

African (AFR) AF: 0.550 AC: 22827 AN: 41472

American (AMR) AF: 0.522 AC: 7969 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3117 AN: 5158

South Asian (SAS) AF: 0.665 AC: 3206 AN: 4824

European-Finnish (FIN) AF: 0.672 AC: 7113 AN: 10590

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48583 AN: 67984

Other (OTH) AF: 0.626 AC: 1320 AN: 2110

Alfa AF: 0.679 Hom.: 49446

Bravo AF: 0.627

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs1378938; hg19: chr15-75096443;