rs7009781

Variant names:

• chr8-53960651-T-C
• rs7009781

Your query was ambiguous. Multiple possible variants found:

• chr8-53960651-T-C
• chr8-53960651-T-G

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 0.385 in 151,870 control chromosomes in the GnomAD database, including 15,964 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 0.38 (15964 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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 (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.384 AC: 58328 AN: 151752 Hom.: 15909 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.385 AC: 58452 AN: 151870 Hom.: 15964 Cov.: 31 AF XY: 0.394 AC XY: 29265 AN XY: 74214

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.363

Alfa AF: 0.210 Hom.: 4865

Bravo AF: 0.405

Asia WGS AF: 0.623 AC: 2167 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	0.14
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7009781; hg19: chr8-54873211;