rs7560236

Variant names:

• chr2-22853911-C-T
• rs7560236

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 0.0269 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0577

Gnomad4 AMR AF: 0.00706

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.00240

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.00655 Hom.: 86

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7560236; hg19: chr2-23076783;