chr2-14572297-T-C

Variant names:

• chr2-14572297-T-C
• rs17348835

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 0.135 in 152,320 control chromosomes in the GnomAD database, including 1,849 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 0.14 (1849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.135 AC: 20590 AN: 152202 Hom.: 1849 Cov.: 33

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.135 AC: 20596 AN: 152320 Hom.: 1849 Cov.: 33 AF XY: 0.138 AC XY: 10311 AN XY: 74476

African (AFR) AF: 0.0339 AC: 1409 AN: 41588

American (AMR) AF: 0.148 AC: 2263 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3472

East Asian (EAS) AF: 0.0877 AC: 455 AN: 5186

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2509 AN: 10606

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11843 AN: 68020

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.158 Hom.: 2618

Bravo AF: 0.121

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.088
DANN	Benign	0.62
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs17348835; hg19: chr2-14712421;