rs7600291

Variant names:

• chr2-73890403-C-G
• rs7600291

Your query was ambiguous. Multiple possible variants found:

• chr2-73890403-C-G
• chr2-73890403-C-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 0.189 in 152,140 control chromosomes in the GnomAD database, including 4,358 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 0.19 (4358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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: 0.189 AC: 28697 AN: 152022 Hom.: 4343 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.189 AC: 28761 AN: 152140 Hom.: 4358 Cov.: 32 AF XY: 0.186 AC XY: 13852 AN XY: 74392

African (AFR) AF: 0.423 AC: 17544 AN: 41472

American (AMR) AF: 0.157 AC: 2401 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3472

East Asian (EAS) AF: 0.0502 AC: 260 AN: 5184

South Asian (SAS) AF: 0.0475 AC: 229 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1327 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6275 AN: 67994

Other (OTH) AF: 0.158 AC: 335 AN: 2116

Alfa AF: 0.144 Hom.: 334

Bravo AF: 0.205

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7600291; hg19: chr2-74117530;