rs7560236

Variant names:

• chr2-22853911-C-T
• rs7560236

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 0.0269 in 152,208 control chromosomes in the GnomAD database, including 159 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 0.027 (159 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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: 0.0269 AC: 4084 AN: 152090 Hom.: 158 Cov.: 31

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00240

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0269 AC: 4093 AN: 152208 Hom.: 159 Cov.: 31 AF XY: 0.0283 AC XY: 2109 AN XY: 74428

African (AFR) AF: 0.0577 AC: 2394 AN: 41514

American (AMR) AF: 0.00706 AC: 108 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.165 AC: 853 AN: 5166

South Asian (SAS) AF: 0.0127 AC: 61 AN: 4820

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10606

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00240 AC: 163 AN: 68024

Other (OTH) AF: 0.0199 AC: 42 AN: 2114

Alfa AF: 0.0106 Hom.: 181

Bravo AF: 0.0263

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	-0.74
CADD	Benign	7.3
DANN	Benign	0.69
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs7560236; hg19: chr2-23076783;