rs1011685

Positions:

• chr8-19973258-C-T

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 0.0881 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.0909

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0885 Hom.: 76

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011685; hg19: chr8-19830769;