rs12617514

Variant names:

• chr2-25196822-C-T
• rs12617514

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 0.221 in 152,096 control chromosomes in the GnomAD database, including 3,989 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 0.22 (3989 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 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: 0.220 AC: 33500 AN: 151978 Hom.: 3973 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.221 AC: 33551 AN: 152096 Hom.: 3989 Cov.: 31 AF XY: 0.229 AC XY: 17042 AN XY: 74344

African (AFR) AF: 0.235 AC: 9752 AN: 41500

American (AMR) AF: 0.351 AC: 5350 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1063 AN: 5184

South Asian (SAS) AF: 0.161 AC: 779 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3006 AN: 10552

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12518 AN: 67988

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.190 Hom.: 1713

Bravo AF: 0.229

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12617514; hg19: chr2-25419691;