rs611203

chr2-218607602-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;