chr2-193626172-G-T

Position:

• chr2-193626172-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.285 in 151,934 control chromosomes in the GnomAD database, including 6,670 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 0.28 (6670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43240 AN: 151814 Hom.: 6662 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43274 AN: 151934 Hom.: 6670 Cov.: 32 AF XY: 0.290 AC XY: 21538 AN XY: 74244

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.298

Alfa AF: 0.308 Hom.: 3898

Bravo AF: 0.289

Asia WGS AF: 0.392 AC: 1359 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497744; hg19: chr2-194490896;