rs10508344

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984206	XR_001747361.2	n.196+1255C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289897	ENST00000701444.2	n.902C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000306499	ENST00000819128.1	n.72-682G>A		intron_variant	Intron 1 of 3
ENSG00000289897	ENST00000819212.1	n.105+1255C>T		intron_variant	Intron 1 of 3

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 v4.3

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;