rs2015178

Variant names:

• chr10-124865002-G-A
• rs2015178

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 0.573 in 152,092 control chromosomes in the GnomAD database, including 27,987 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 0.57 (27987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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: 0.573 AC: 87100 AN: 151974 Hom.: 27970 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.573 AC: 87138 AN: 152092 Hom.: 27987 Cov.: 33 AF XY: 0.578 AC XY: 42984 AN XY: 74378

African (AFR) AF: 0.254 AC: 10534 AN: 41468

American (AMR) AF: 0.671 AC: 10255 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2410 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3177 AN: 5166

South Asian (SAS) AF: 0.670 AC: 3232 AN: 4822

European-Finnish (FIN) AF: 0.708 AC: 7495 AN: 10588

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.705 AC: 47958 AN: 67988

Other (OTH) AF: 0.600 AC: 1267 AN: 2112

Alfa AF: 0.661 Hom.: 129506

Bravo AF: 0.553

Asia WGS AF: 0.606 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	16
DANN	Benign	0.64
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs2015178; hg19: chr10-126553571;