rs12602486

Variant names:

• chr17-44164561-T-G
• rs12602486

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 0.0377 in 152,268 control chromosomes in the GnomAD database, including 139 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 0.038 (139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0627 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: 0.0377 AC: 5742 AN: 152150 Hom.: 138 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0377 AC: 5747 AN: 152268 Hom.: 139 Cov.: 31 AF XY: 0.0373 AC XY: 2780 AN XY: 74458

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.0329

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0361 Hom.: 27

Bravo AF: 0.0413

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12602486; hg19: chr17-42241929;