rs1563512

Variant names:

• chr6-122158600-G-A
• rs1563512

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 0.343 in 151,984 control chromosomes in the GnomAD database, including 9,456 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 0.34 (9456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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 (SAS) allele frequency at 95% confidence interval = 0.483 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: 0.344 AC: 52186 AN: 151864 Hom.: 9452 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.343 AC: 52204 AN: 151984 Hom.: 9456 Cov.: 32 AF XY: 0.354 AC XY: 26308 AN XY: 74258

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.348

Alfa AF: 0.322 Hom.: 996

Bravo AF: 0.348

Asia WGS AF: 0.418 AC: 1451 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	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1563512; hg19: chr6-122479746;