chr10-116539194-C-T

Variant names:

• chr10-116539194-C-T
• rs12249434

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 0.0813 in 151,742 control chromosomes in the GnomAD database, including 558 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 0.081 (558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0875 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: 0.0813 AC: 12328 AN: 151638 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0813 AC: 12338 AN: 151742 Hom.: 558 Cov.: 32 AF XY: 0.0804 AC XY: 5960 AN XY: 74120

African (AFR) AF: 0.0899 AC: 3719 AN: 41386

American (AMR) AF: 0.0613 AC: 934 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0915 AC: 439 AN: 4798

European-Finnish (FIN) AF: 0.0581 AC: 608 AN: 10460

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0893 AC: 6064 AN: 67914

Other (OTH) AF: 0.0795 AC: 167 AN: 2100

Alfa AF: 0.0900 Hom.: 1168

Bravo AF: 0.0797

Asia WGS AF: 0.0380 AC: 130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs12249434; hg19: chr10-118298706;