rs7009781

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;