rs1512225

Positions:

• chr2-60258458-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 0.0402 in 152,260 control chromosomes in the GnomAD database, including 196 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 0.040 (196 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 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: 0.0402 AC: 6110 AN: 152142 Hom.: 196 Cov.: 33

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0402 AC: 6115 AN: 152260 Hom.: 196 Cov.: 33 AF XY: 0.0397 AC XY: 2959 AN XY: 74464

Gnomad4 AFR AF: 0.0779

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0311 Hom.: 18

Bravo AF: 0.0406

Asia WGS AF: 0.0650 AC: 226 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	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512225; hg19: chr2-60485593;