rs12602486

chr17-44164561-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;