rs2609101

Variant names:

• chr2-6045502-A-C
• rs2609101

Your query was ambiguous. Multiple possible variants found:

• chr2-6045502-A-C
• chr2-6045502-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;