9-7518656-T-C

Variant names:

• chr9-7518656-T-C
• rs2381628

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 0.767 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.751

Alfa AF: 0.789 Hom.: 37764

Bravo AF: 0.760

Asia WGS AF: 0.895 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381628; hg19: chr9-7518656;