rs2453836

chr7-45926196-A-G

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 0.187 in 151,820 control chromosomes in the GnomAD database, including 2,788 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 (2788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28353 AN: 151700 Hom.: 2782 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.187 AC: 28388 AN: 151820 Hom.: 2788 Cov.: 32 AF XY: 0.185 AC XY: 13734 AN XY: 74178

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.227

Alfa AF: 0.192 Hom.: 5997

Bravo AF: 0.188

Asia WGS AF: 0.197 AC: 684 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2453836; hg19: chr7-45965795;