rs9969309

Positions:

• chr7-150751959-G-A

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 0.216 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

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 (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.216 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

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.177

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9969309; hg19: chr7-150449047;