rs7577262

Variant names:

• chr2-233910224-G-A
• rs7577262

Your query was ambiguous. Multiple possible variants found:

• chr2-233910224-G-A
• chr2-233910224-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 0.16 in 152,144 control chromosomes in the GnomAD database, including 2,562 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 0.16 (2562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 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: 0.160 AC: 24312 AN: 152026 Hom.: 2556 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.0584

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.160 AC: 24356 AN: 152144 Hom.: 2562 Cov.: 32 AF XY: 0.160 AC XY: 11868 AN XY: 74384

African (AFR) AF: 0.260 AC: 10795 AN: 41462

American (AMR) AF: 0.0937 AC: 1432 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1985 AN: 5174

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4816

European-Finnish (FIN) AF: 0.0584 AC: 620 AN: 10608

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7398 AN: 68008

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.130 Hom.: 3406

Bravo AF: 0.168

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.079
DANN	Benign	0.60
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7577262; hg19: chr2-234818869;