12-42737731-T-G

Variant names:

• chr12-42737731-T-G
• rs1517661

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 0.47 in 152,230 control chromosomes in the GnomAD database, including 17,317 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 0.47 (17317 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.471 AC: 71593 AN: 152112 Hom.: 17324 Cov.: 34

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.470 AC: 71611 AN: 152230 Hom.: 17317 Cov.: 34 AF XY: 0.468 AC XY: 34815 AN XY: 74426

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.524

Alfa AF: 0.491 Hom.: 5480

Bravo AF: 0.492

Asia WGS AF: 0.431 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517661; hg19: chr12-43131533;