rs1015151

Positions:

• chr20-6709855-T-A
• chr20-6709855-T-C
• chr20-6709855-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 0.53 in 151,974 control chromosomes in the GnomAD database, including 21,846 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 0.53 (21846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80383 AN: 151856 Hom.: 21815 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.530 AC: 80475 AN: 151974 Hom.: 21846 Cov.: 32 AF XY: 0.534 AC XY: 39641 AN XY: 74288

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.525

Alfa AF: 0.504 Hom.: 2399

Bravo AF: 0.543

Asia WGS AF: 0.645 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015151; hg19: chr20-6690502;