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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.415

Alfa AF: 0.395 Hom.: 21095

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7171749; hg19: chr15-78708715;