10-121293214-C-T

Variant names:

• chr10-121293214-C-T
• rs12413088
• ENST00000778913.1:n.177-1523G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000778913.1(ENSG00000301448):​n.177-1523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,080 control chromosomes in the GnomAD database, including 2,995 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 0.18 (2995 hom., cov: 32)
• Consequence: ENSG00000301448 ENST00000778913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 5 publications found

Genes affected

ENSG00000301448 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778913.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000301448	ENST00000778913.1		n.177-1523G>A		intron	N/A
	ENSG00000301448	ENST00000778914.1		n.492-1523G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27052 AN: 151962 Hom.: 2997 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.178 AC: 27051 AN: 152080 Hom.: 2995 Cov.: 32 AF XY: 0.179 AC XY: 13329 AN XY: 74346

African (AFR) AF: 0.0512 AC: 2124 AN: 41508

American (AMR) AF: 0.184 AC: 2813 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3470

East Asian (EAS) AF: 0.155 AC: 801 AN: 5180

South Asian (SAS) AF: 0.162 AC: 780 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3120 AN: 10564

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15502 AN: 67946

Other (OTH) AF: 0.205 AC: 432 AN: 2112

Alfa AF: 0.214 Hom.: 2947

Bravo AF: 0.165

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.61
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs12413088; hg19: chr10-123052728;