rs1102563

Variant names:

• chr6-27192316-A-G
• rs1102563

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;