rs7178239

Variant names:

• chr15-101267907-C-G
• rs7178239

Your query was ambiguous. Multiple possible variants found:

• chr15-101267907-C-G
• chr15-101267907-C-T

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 0.357 in 151,964 control chromosomes in the GnomAD database, including 14,773 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 0.36 (14773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.357 AC: 54186 AN: 151844 Hom.: 14724 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.357 AC: 54302 AN: 151964 Hom.: 14773 Cov.: 32 AF XY: 0.356 AC XY: 26410 AN XY: 74238

African (AFR) AF: 0.758 AC: 31411 AN: 41452

American (AMR) AF: 0.343 AC: 5236 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2135 AN: 5138

South Asian (SAS) AF: 0.118 AC: 571 AN: 4820

European-Finnish (FIN) AF: 0.223 AC: 2350 AN: 10546

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11230 AN: 67960

Other (OTH) AF: 0.316 AC: 666 AN: 2106

Alfa AF: 0.128 Hom.: 315

Bravo AF: 0.391

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs7178239; hg19: chr15-101808112;