chr9-7518656-T-C

Variant names:

• chr9-7518656-T-C
• rs2381628

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 0.767 in 152,114 control chromosomes in the GnomAD database, including 45,214 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 0.77 (45214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.767 AC: 116551 AN: 151996 Hom.: 45194 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.767 AC: 116621 AN: 152114 Hom.: 45214 Cov.: 32 AF XY: 0.771 AC XY: 57348 AN XY: 74372

African (AFR) AF: 0.638 AC: 26439 AN: 41450

American (AMR) AF: 0.805 AC: 12315 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2653 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4969 AN: 5182

South Asian (SAS) AF: 0.864 AC: 4165 AN: 4818

European-Finnish (FIN) AF: 0.826 AC: 8751 AN: 10592

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54797 AN: 67992

Other (OTH) AF: 0.751 AC: 1587 AN: 2114

Alfa AF: 0.772 Hom.: 63464

Bravo AF: 0.760

Asia WGS AF: 0.895 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.53
DANN	Benign	0.57
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2381628; hg19: chr9-7518656;