rs611203

Variant names:

• chr2-218607602-G-A
• rs611203

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 0.596 in 152,178 control chromosomes in the GnomAD database, including 27,228 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 0.60 (27228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.596 AC: 90646 AN: 152060 Hom.: 27205 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.596 AC: 90713 AN: 152178 Hom.: 27228 Cov.: 33 AF XY: 0.600 AC XY: 44661 AN XY: 74402

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.617

Alfa AF: 0.583 Hom.: 24928

Bravo AF: 0.596

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs611203; hg19: chr2-219472325;