rs7177250

Variant names:

• chr15-69146204-T-A
• rs7177250

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 0.224 in 152,196 control chromosomes in the GnomAD database, including 5,930 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 0.22 (5930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.224 AC: 34050 AN: 152076 Hom.: 5891 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.224 AC: 34141 AN: 152196 Hom.: 5930 Cov.: 32 AF XY: 0.221 AC XY: 16457 AN XY: 74418

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.189

Alfa AF: 0.185 Hom.: 511

Bravo AF: 0.239

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7177250; hg19: chr15-69438543;