chr2-189627288-T-C

Variant names:

• chr2-189627288-T-C
• rs10497705

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 0.353 in 151,870 control chromosomes in the GnomAD database, including 10,812 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 (10812 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.353 AC: 53603 AN: 151752 Hom.: 10796 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.353 AC: 53635 AN: 151870 Hom.: 10812 Cov.: 30 AF XY: 0.366 AC XY: 27147 AN XY: 74210

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.332

Alfa AF: 0.351 Hom.: 13679

Bravo AF: 0.346

Asia WGS AF: 0.594 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
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: rs10497705; hg19: chr2-190492014;