12-39028488-A-T

Variant names:

• chr12-39028488-A-T
• rs10876410

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 0.497 in 152,010 control chromosomes in the GnomAD database, including 19,860 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 0.50 (19860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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 (NFE) allele frequency at 95% confidence interval = 0.575 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: 0.497 AC: 75442 AN: 151892 Hom.: 19847 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.0665

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.497 AC: 75495 AN: 152010 Hom.: 19860 Cov.: 32 AF XY: 0.491 AC XY: 36439 AN XY: 74282

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.471

Alfa AF: 0.401 Hom.: 1072

Bravo AF: 0.488

Asia WGS AF: 0.196 AC: 689 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	0.96
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10876410; hg19: chr12-39422290;