chr10-8180249-G-A

Variant names:

• chr10-8180249-G-A
• rs10508344
• ENST00000701444.2:n.902C>T

Variant summary

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

The ENST00000701444.2(ENSG00000289897):​n.902C>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 0.0792 in 151,902 control chromosomes in the GnomAD database, including 614 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 0.079 (614 hom., cov: 32)
• Consequence: ENSG00000289897 ENST00000701444.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 5 publications found

Genes affected

ENSG00000289897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701444.2. 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
	ENSG00000289897	ENST00000701444.2		n.902C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000306499	ENST00000819128.1		n.72-682G>A		intron	N/A
	ENSG00000289897	ENST00000819212.1		n.105+1255C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12019 AN: 151784 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.0852

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0792 AC: 12025 AN: 151902 Hom.: 614 Cov.: 32 AF XY: 0.0815 AC XY: 6052 AN XY: 74266

African (AFR) AF: 0.0214 AC: 886 AN: 41488

American (AMR) AF: 0.0896 AC: 1365 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0852 AC: 295 AN: 3464

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5184

South Asian (SAS) AF: 0.106 AC: 513 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10566

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7140 AN: 67836

Other (OTH) AF: 0.0799 AC: 168 AN: 2102

Alfa AF: 0.101 Hom.: 531

Bravo AF: 0.0722

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10508344; hg19: chr10-8222212;