chr2-229744433-C-T

Variant names:

• chr2-229744433-C-T
• rs6707272

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 0.319 in 152,118 control chromosomes in the GnomAD database, including 8,112 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 0.32 (8112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.319 AC: 48492 AN: 152000 Hom.: 8102 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.319 AC: 48532 AN: 152118 Hom.: 8112 Cov.: 33 AF XY: 0.313 AC XY: 23256 AN XY: 74368

African (AFR) AF: 0.397 AC: 16462 AN: 41464

American (AMR) AF: 0.283 AC: 4326 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1414 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1199 AN: 5186

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1992 AN: 10584

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20667 AN: 67984

Other (OTH) AF: 0.318 AC: 670 AN: 2110

Alfa AF: 0.309 Hom.: 20325

Bravo AF: 0.325

Asia WGS AF: 0.258 AC: 896 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	1.3
DANN	Benign	0.31
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs6707272; hg19: chr2-230609149; COSMIC: COSV53448533;