chr7-150986541-G-T

Position:

• chr7-150986541-G-T

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 0.345 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.150986541G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.334

Alfa AF: 0.288 Hom.: 1771

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12703107; hg19: chr7-150683629;