7-150566065-G-C

Position:

• chr7-150566065-G-C

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 0.253 in 152,052 control chromosomes in the GnomAD database, including 5,060 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 0.25 (5060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38437 AN: 151932 Hom.: 5048 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.253 AC: 38487 AN: 152052 Hom.: 5060 Cov.: 32 AF XY: 0.254 AC XY: 18886 AN XY: 74310

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.235

Alfa AF: 0.238 Hom.: 564

Bravo AF: 0.256

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10273606; hg19: chr7-150263153;