7-150751959-G-A

Variant names:

• chr7-150751959-G-A
• rs9969309

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 0.216 in 152,086 control chromosomes in the GnomAD database, including 4,336 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 0.22 (4336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.216 AC: 32769 AN: 151968 Hom.: 4324 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0903

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.216 AC: 32832 AN: 152086 Hom.: 4336 Cov.: 32 AF XY: 0.220 AC XY: 16356 AN XY: 74330

African (AFR) AF: 0.363 AC: 15043 AN: 41480

American (AMR) AF: 0.150 AC: 2286 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5180

South Asian (SAS) AF: 0.158 AC: 761 AN: 4826

European-Finnish (FIN) AF: 0.274 AC: 2889 AN: 10542

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9451 AN: 67980

Other (OTH) AF: 0.177 AC: 375 AN: 2116

Alfa AF: 0.192 Hom.: 411

Bravo AF: 0.214

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.68
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9969309; hg19: chr7-150449047;