rs793108

chr10-31126177-C-T

Variant summary

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

The ENST00000658872.1(ENSG00000287564):n.510-17562C>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 0.405 in 151,998 control chromosomes in the GnomAD database, including 14,352 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 0.40 (14352 hom., cov: 32)
• Consequence: ENST00000658872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376481	XR_001747410.3	n.2981+20052C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658872.1	n.510-17562C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61522 AN: 151878 Hom.: 14350 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.405 AC: 61529 AN: 151998 Hom.: 14352 Cov.: 32 AF XY: 0.410 AC XY: 30476 AN XY: 74302

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.393

Alfa AF: 0.468 Hom.: 6883

Bravo AF: 0.389

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.9
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs793108; hg19: chr10-31415106;