13-106403247-A-T

Variant names:

• chr13-106403247-A-T
• rs10492641
• ENST00000753311.1:n.149-1707T>A

Variant summary

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

The ENST00000753311.1(ENSG00000298145):​n.149-1707T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,076 control chromosomes in the GnomAD database, including 9,059 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 0.33 (9059 hom., cov: 32)
• Consequence: ENSG00000298145 ENST00000753311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29
• Publications: 1 publications found

Genes affected

ENSG00000298145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298145	ENST00000753311.1		n.149-1707T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50399 AN: 151958 Hom.: 9064 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.331 AC: 50397 AN: 152076 Hom.: 9059 Cov.: 32 AF XY: 0.327 AC XY: 24299 AN XY: 74370

African (AFR) AF: 0.209 AC: 8683 AN: 41498

American (AMR) AF: 0.304 AC: 4651 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3466

East Asian (EAS) AF: 0.124 AC: 641 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1285 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4224 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28652 AN: 67950

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.237 Hom.: 592

Bravo AF: 0.319

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	19
DANN	Benign	0.67
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs10492641; hg19: chr13-107055595;