chr7-150362325-C-T

Variant names:

• chr7-150362325-C-T
• rs17173681

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 0.226 in 152,044 control chromosomes in the GnomAD database, including 4,719 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 0.23 (4719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.226 AC: 34353 AN: 151926 Hom.: 4726 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.226 AC: 34340 AN: 152044 Hom.: 4719 Cov.: 32 AF XY: 0.233 AC XY: 17288 AN XY: 74284

African (AFR) AF: 0.0731 AC: 3032 AN: 41490

American (AMR) AF: 0.188 AC: 2867 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3466

East Asian (EAS) AF: 0.435 AC: 2240 AN: 5150

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3596 AN: 10544

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18922 AN: 67998

Other (OTH) AF: 0.216 AC: 455 AN: 2110

Alfa AF: 0.239 Hom.: 815

Bravo AF: 0.207

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.38
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs17173681; hg19: chr7-150059414;