2-194661877-G-T

Variant names:

• chr2-194661877-G-T
• rs10489996

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0937 in 152,130 control chromosomes in the GnomAD database, including 1,373 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 0.094 (1373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.0935 AC: 14210 AN: 152012 Hom.: 1364 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0937 AC: 14248 AN: 152130 Hom.: 1373 Cov.: 32 AF XY: 0.0915 AC XY: 6803 AN XY: 74382

African (AFR) AF: 0.255 AC: 10572 AN: 41476

American (AMR) AF: 0.0430 AC: 657 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3472

East Asian (EAS) AF: 0.0873 AC: 451 AN: 5168

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4830

European-Finnish (FIN) AF: 0.0277 AC: 294 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1858 AN: 67982

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0124 Hom.: 5

Bravo AF: 0.102

Asia WGS AF: 0.0650 AC: 224 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.43
DANN	Benign	0.15
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10489996; hg19: chr2-195526601;