rs10847578

Positions:

• chr12-128222342-T-C

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 0.446 in 152,074 control chromosomes in the GnomAD database, including 15,508 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 0.45 (15508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.446 AC: 67794 AN: 151956 Hom.: 15496 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.446 AC: 67848 AN: 152074 Hom.: 15508 Cov.: 32 AF XY: 0.451 AC XY: 33500 AN XY: 74322

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.451

Alfa AF: 0.477 Hom.: 30074

Bravo AF: 0.433

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10847578; hg19: chr12-128706887;