rs1008563

Variant names:

• chr2-218162165-G-A
• rs1008563

Your query was ambiguous. Multiple possible variants found:

• chr2-218162165-G-A
• chr2-218162165-G-C

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 0.43 in 150,448 control chromosomes in the GnomAD database, including 14,937 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 0.43 (14937 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.430 AC: 64668 AN: 150332 Hom.: 14927 Cov.: 30

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.430 AC: 64707 AN: 150448 Hom.: 14937 Cov.: 30 AF XY: 0.424 AC XY: 31143 AN XY: 73474

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.474

Alfa AF: 0.442 Hom.: 19016

Bravo AF: 0.436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008563; hg19: chr2-219026888;