rs2609101

chr2-6045502-A-Cchr2-6045502-A-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 0.351 in 151,904 control chromosomes in the GnomAD database, including 13,053 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 0.35 (13053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.351 AC: 53216 AN: 151786 Hom.: 13007 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.351 AC: 53315 AN: 151904 Hom.: 13053 Cov.: 32 AF XY: 0.348 AC XY: 25832 AN XY: 74250

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.329

Alfa AF: 0.220 Hom.: 8497

Bravo AF: 0.364

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.41
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2609101; hg19: chr2-6185634;