rs10847578

Variant names:

• chr12-128222342-T-C
• rs10847578

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.329 AC: 13651 AN: 41476

American (AMR) AF: 0.476 AC: 7279 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2152 AN: 5168

South Asian (SAS) AF: 0.480 AC: 2312 AN: 4816

European-Finnish (FIN) AF: 0.573 AC: 6056 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33233 AN: 67960

Other (OTH) AF: 0.451 AC: 950 AN: 2108

Alfa AF: 0.472 Hom.: 65857

Bravo AF: 0.433

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10847578; hg19: chr12-128706887;