rs611203

Variant names:

• chr2-218607602-G-A
• rs611203

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.589 AC: 24473 AN: 41518

American (AMR) AF: 0.611 AC: 9341 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4039 AN: 5178

South Asian (SAS) AF: 0.684 AC: 3303 AN: 4830

European-Finnish (FIN) AF: 0.573 AC: 6068 AN: 10588

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39275 AN: 67994

Other (OTH) AF: 0.617 AC: 1300 AN: 2108

Alfa AF: 0.586 Hom.: 63189

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
PhyloP100		0.62
PromoterAI		-0.085	Neutral

Splicing

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

Other links and lift over

dbSNP: rs611203; hg19: chr2-219472325;