rs1102563

Positions:

• chr6-27192316-A-G
• chr6-27192316-A-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 0.606 in 151,964 control chromosomes in the GnomAD database, including 31,363 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 0.61 (31363 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.606 AC: 92037 AN: 151846 Hom.: 31358 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.606 AC: 92055 AN: 151964 Hom.: 31363 Cov.: 31 AF XY: 0.603 AC XY: 44758 AN XY: 74258

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.605

Alfa AF: 0.732 Hom.: 53798

Bravo AF: 0.590

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
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: rs1102563; hg19: chr6-27160095;