7-150987742-C-A

Variant names:

• chr7-150987742-C-A
• rs10952296

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 0.336 in 151,732 control chromosomes in the GnomAD database, including 9,706 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 0.34 (9706 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50976 AN: 151614 Hom.: 9676 Cov.: 30

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.336 AC: 51050 AN: 151732 Hom.: 9706 Cov.: 30 AF XY: 0.345 AC XY: 25555 AN XY: 74140

African (AFR) AF: 0.438 AC: 18089 AN: 41296

American (AMR) AF: 0.367 AC: 5608 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3859 AN: 5142

South Asian (SAS) AF: 0.452 AC: 2172 AN: 4806

European-Finnish (FIN) AF: 0.300 AC: 3154 AN: 10526

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16072 AN: 67916

Other (OTH) AF: 0.324 AC: 681 AN: 2104

Alfa AF: 0.294 Hom.: 4284

Bravo AF: 0.350

Asia WGS AF: 0.588 AC: 2039 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs10952296; hg19: chr7-150684830;