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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.112 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

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0948

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.133

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2567603; hg19: chr2-73986125;