rs12617514

chr2-25196822-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.206

Alfa AF: 0.191 Hom.: 1611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12617514; hg19: chr2-25419691;