7-150986541-G-T

Variant names:

• chr7-150986541-G-T
• rs12703107

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 0.345 in 152,008 control chromosomes in the GnomAD database, including 10,339 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 0.35 (10339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.345 AC: 52394 AN: 151890 Hom.: 10309 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.345 AC: 52462 AN: 152008 Hom.: 10339 Cov.: 32 AF XY: 0.353 AC XY: 26224 AN XY: 74260

African (AFR) AF: 0.467 AC: 19334 AN: 41438

American (AMR) AF: 0.369 AC: 5646 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3880 AN: 5156

South Asian (SAS) AF: 0.422 AC: 2035 AN: 4822

European-Finnish (FIN) AF: 0.300 AC: 3171 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16243 AN: 67952

Other (OTH) AF: 0.334 AC: 704 AN: 2108

Alfa AF: 0.276 Hom.: 2914

Bravo AF: 0.360

Asia WGS AF: 0.580 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs12703107; hg19: chr7-150683629;