rs2730078

Variant names:

• chr15-83652677-A-G
• rs2730078

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 0.209 in 152,114 control chromosomes in the GnomAD database, including 4,347 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 0.21 (4347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 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: 0.209 AC: 31742 AN: 151994 Hom.: 4342 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.209 AC: 31748 AN: 152114 Hom.: 4347 Cov.: 32 AF XY: 0.207 AC XY: 15384 AN XY: 74366

African (AFR) AF: 0.0510 AC: 2119 AN: 41522

American (AMR) AF: 0.346 AC: 5293 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3470

East Asian (EAS) AF: 0.0684 AC: 354 AN: 5174

South Asian (SAS) AF: 0.134 AC: 644 AN: 4806

European-Finnish (FIN) AF: 0.247 AC: 2613 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18612 AN: 67980

Other (OTH) AF: 0.248 AC: 521 AN: 2102

Alfa AF: 0.257 Hom.: 15196

Bravo AF: 0.213

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs2730078; hg19: chr15-84321429;