rs1011685

Variant names:

• chr8-19973258-C-T
• rs1011685

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 0.0881 in 152,240 control chromosomes in the GnomAD database, including 589 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 0.088 (589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 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: 0.0882 AC: 13420 AN: 152122 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0881 AC: 13409 AN: 152240 Hom.: 589 Cov.: 32 AF XY: 0.0874 AC XY: 6507 AN XY: 74426

African (AFR) AF: 0.0631 AC: 2620 AN: 41530

American (AMR) AF: 0.0799 AC: 1222 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.108 AC: 556 AN: 5172

South Asian (SAS) AF: 0.0961 AC: 464 AN: 4830

European-Finnish (FIN) AF: 0.0909 AC: 964 AN: 10608

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6866 AN: 68024

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.0884 Hom.: 79

Bravo AF: 0.0855

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.26
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1011685; hg19: chr8-19830769;