rs2567603

Variant names:

• chr2-73758998-G-C
• rs2567603

Your query was ambiguous. Multiple possible variants found:

• chr2-73758998-G-C
• chr2-73758998-G-T

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 0.112 in 152,238 control chromosomes in the GnomAD database, including 1,247 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 0.11 (1247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17090 AN: 152120 Hom.: 1247 Cov.: 32

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.112 AC: 17090 AN: 152238 Hom.: 1247 Cov.: 32 AF XY: 0.108 AC XY: 8060 AN XY: 74432

African (AFR) AF: 0.0303 AC: 1261 AN: 41554

American (AMR) AF: 0.177 AC: 2708 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5186

South Asian (SAS) AF: 0.0948 AC: 457 AN: 4822

European-Finnish (FIN) AF: 0.0848 AC: 898 AN: 10590

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10795 AN: 68006

Other (OTH) AF: 0.133 AC: 281 AN: 2116

Alfa AF: 0.0708 Hom.: 113

Bravo AF: 0.117

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.63
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2567603; hg19: chr2-73986125;