rs7560236

Positions:

• chr2-22853911-C-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 0.0269 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;