rs10879618

Variant names:

• chr12-73496875-T-C
• rs10879618

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 0.39 in 152,006 control chromosomes in the GnomAD database, including 11,784 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 0.39 (11784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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: 0.390 AC: 59240 AN: 151888 Hom.: 11770 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.390 AC: 59294 AN: 152006 Hom.: 11784 Cov.: 32 AF XY: 0.393 AC XY: 29164 AN XY: 74298

African (AFR) AF: 0.342 AC: 14195 AN: 41474

American (AMR) AF: 0.430 AC: 6559 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5164

South Asian (SAS) AF: 0.397 AC: 1915 AN: 4824

European-Finnish (FIN) AF: 0.469 AC: 4954 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27624 AN: 67932

Other (OTH) AF: 0.376 AC: 795 AN: 2114

Alfa AF: 0.406 Hom.: 6687

Bravo AF: 0.385

Asia WGS AF: 0.317 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10879618; hg19: chr12-73890655;