10-117582309-C-T

Position:

• chr10-117582309-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000672708.1(ENSG00000288172):​n.73+2383C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 151,980 control chromosomes in the GnomAD database, including 44,211 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 0.76 (44211 hom., cov: 31)
• Consequence: ENST00000672708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000672708.1	n.73+2383C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115041 AN: 151862 Hom.: 44151 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.758 AC: 115164 AN: 151980 Hom.: 44211 Cov.: 31 AF XY: 0.757 AC XY: 56228 AN XY: 74254

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.801

Alfa AF: 0.799 Hom.: 96992

Bravo AF: 0.758

Asia WGS AF: 0.716 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703361; hg19: chr10-119341820;