ENST00000744253.1:n.74C>T

Variant names:

• chr6-105799262-C-T
• rs10499043
• ENST00000744253.1:n.74C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000744253.1(ENSG00000297010):​n.74C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,244 control chromosomes in the GnomAD database, including 642 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 0.087 (642 hom., cov: 32)
• Consequence: ENSG00000297010 ENST00000744253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.985
• Publications: 6 publications found

Genes affected

ENSG00000297010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744253.1. 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
	ENSG00000297010	ENST00000744253.1		n.74C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000284999	ENST00000644129.1		n.281+30795G>A		intron	N/A
	ENSG00000284999	ENST00000744159.1		n.375-29667G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13296 AN: 152126 Hom.: 643 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0873 AC: 13290 AN: 152244 Hom.: 642 Cov.: 32 AF XY: 0.0854 AC XY: 6355 AN XY: 74438

African (AFR) AF: 0.0384 AC: 1596 AN: 41552

American (AMR) AF: 0.0942 AC: 1441 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.0961 AC: 498 AN: 5184

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4820

European-Finnish (FIN) AF: 0.0608 AC: 645 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7885 AN: 68006

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.104 Hom.: 1343

Bravo AF: 0.0881

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	17
DANN	Benign	0.54
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs10499043; hg19: chr6-106247137;