rs10842178

Variant names:

• chr12-23524423-T-C
• rs10842178

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 0.252 in 152,118 control chromosomes in the GnomAD database, including 5,691 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 0.25 (5691 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.252 AC: 38245 AN: 152000 Hom.: 5687 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.252 AC: 38258 AN: 152118 Hom.: 5691 Cov.: 33 AF XY: 0.250 AC XY: 18604 AN XY: 74362

African (AFR) AF: 0.104 AC: 4337 AN: 41546

American (AMR) AF: 0.255 AC: 3888 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3466

East Asian (EAS) AF: 0.523 AC: 2700 AN: 5160

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4824

European-Finnish (FIN) AF: 0.223 AC: 2359 AN: 10580

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20328 AN: 67960

Other (OTH) AF: 0.294 AC: 620 AN: 2106

Alfa AF: 0.284 Hom.: 2939

Bravo AF: 0.248

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.68
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10842178; hg19: chr12-23677357;