rs2897305

chr4-136678862-C-A

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 0.241 in 151,512 control chromosomes in the GnomAD database, including 4,458 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 0.24 (4458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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: 0.241 AC: 36424 AN: 151398 Hom.: 4456 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.241 AC: 36455 AN: 151512 Hom.: 4458 Cov.: 32 AF XY: 0.240 AC XY: 17796 AN XY: 74022

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.230

Alfa AF: 0.255 Hom.: 2285

Bravo AF: 0.234

Asia WGS AF: 0.239 AC: 831 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.55
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2897305; hg19: chr4-137600017;