rs1380642

Variant names:

• chr15-79804529-C-T
• rs1380642

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 0.171 in 152,182 control chromosomes in the GnomAD database, including 2,374 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 0.17 (2374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 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: 0.171 AC: 26043 AN: 152064 Hom.: 2370 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.171 AC: 26066 AN: 152182 Hom.: 2374 Cov.: 33 AF XY: 0.171 AC XY: 12734 AN XY: 74414

African (AFR) AF: 0.122 AC: 5082 AN: 41520

American (AMR) AF: 0.153 AC: 2332 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.147 AC: 760 AN: 5184

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67990

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.190 Hom.: 4768

Bravo AF: 0.166

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1380642; hg19: chr15-80096871;