rs7171749

Variant names:

• chr15-78416373-T-C
• rs7171749

Your query was ambiguous. Multiple possible variants found:

• chr15-78416373-T-C
• chr15-78416373-T-G

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 0.407 in 151,814 control chromosomes in the GnomAD database, including 12,919 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 0.41 (12919 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 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: 0.407 AC: 61667 AN: 151696 Hom.: 12895 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.407 AC: 61757 AN: 151814 Hom.: 12919 Cov.: 31 AF XY: 0.406 AC XY: 30144 AN XY: 74198

African (AFR) AF: 0.427 AC: 17683 AN: 41382

American (AMR) AF: 0.517 AC: 7878 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1437 AN: 3464

East Asian (EAS) AF: 0.525 AC: 2697 AN: 5136

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4816

European-Finnish (FIN) AF: 0.323 AC: 3401 AN: 10538

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25535 AN: 67928

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.395 Hom.: 46759

Bravo AF: 0.425

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.7
DANN	Benign	0.58
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7171749; hg19: chr15-78708715;