rs10879490

Positions:

• chr12-72769371-T-A

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 0.299 in 152,094 control chromosomes in the GnomAD database, including 9,213 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 0.30 (9213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.300 AC: 45552 AN: 151976 Hom.: 9216 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.299 AC: 45540 AN: 152094 Hom.: 9213 Cov.: 32 AF XY: 0.302 AC XY: 22464 AN XY: 74338

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.300

Alfa AF: 0.364 Hom.: 1514

Bravo AF: 0.268

Asia WGS AF: 0.110 AC: 381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10879490; hg19: chr12-73163151;