7-150344747-T-G

Position:

• chr7-150344747-T-G

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 0.262 in 151,650 control chromosomes in the GnomAD database, including 5,304 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 0.26 (5304 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150344747T>G		intergenic_region
LOC107986858	XR_001745420.3	n.607+1106T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39745 AN: 151538 Hom.: 5300 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 151650 Hom.: 5304 Cov.: 31 AF XY: 0.261 AC XY: 19355 AN XY: 74090

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.236

Alfa AF: 0.146 Hom.: 266

Bravo AF: 0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6964110; hg19: chr7-150041836;