7-150914073-G-T

Variant names:

• chr7-150914073-G-T
• rs17173658

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 0.0658 in 152,096 control chromosomes in the GnomAD database, including 660 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 0.066 (660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 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: 0.0656 AC: 9974 AN: 151978 Hom.: 646 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0769

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

GnomAD4 genome AF: 0.0658 AC: 10011 AN: 152096 Hom.: 660 Cov.: 32 AF XY: 0.0720 AC XY: 5355 AN XY: 74342

African (AFR) AF: 0.0160 AC: 663 AN: 41494

American (AMR) AF: 0.191 AC: 2912 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1269 AN: 5170

South Asian (SAS) AF: 0.108 AC: 520 AN: 4812

European-Finnish (FIN) AF: 0.0901 AC: 952 AN: 10570

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3133 AN: 67976

Other (OTH) AF: 0.0818 AC: 173 AN: 2116

Alfa AF: 0.0603 Hom.: 1014

Bravo AF: 0.0727

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs17173658; hg19: chr7-150611161;