10-114041494-T-C

Variant names:

• chr10-114041494-T-C
• rs2429511
• ENST00000730109.1:n.79T>C

Variant summary

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

The ENST00000730109.1(ENSG00000295437):​n.79T>C 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 0.43 in 152,060 control chromosomes in the GnomAD database, including 14,780 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 0.43 (14780 hom., cov: 33)
• Consequence: ENSG00000295437 ENST00000730109.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 5 publications found

Genes affected

ENSG00000295437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730109.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295437	ENST00000730109.1		n.79T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000295421	ENST00000729868.1		n.293-641A>G		intron	N/A
	ENSG00000295421	ENST00000729869.1		n.124+1500A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65346 AN: 151942 Hom.: 14785 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.430 AC: 65358 AN: 152060 Hom.: 14780 Cov.: 33 AF XY: 0.435 AC XY: 32310 AN XY: 74314

African (AFR) AF: 0.283 AC: 11743 AN: 41474

American (AMR) AF: 0.458 AC: 7004 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3189 AN: 5168

South Asian (SAS) AF: 0.563 AC: 2718 AN: 4828

European-Finnish (FIN) AF: 0.490 AC: 5171 AN: 10554

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32496 AN: 67970

Other (OTH) AF: 0.421 AC: 889 AN: 2112

Alfa AF: 0.461 Hom.: 26395

Bravo AF: 0.417

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.21
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2429511; hg19: chr10-115801253;