rs2793109

chr10-31090917-T-A

Variant summary

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

The ENST00000658872.1(ENSG00000287564):n.323-15022T>A 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 0.401 in 152,036 control chromosomes in the GnomAD database, including 14,214 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 (14214 hom., cov: 31)
• Consequence: ENST00000658872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376481	XR_001747410.3	n.2795-15022T>A		intron_variant, non_coding_transcript_variant
LOC105376481	XR_001747409.3	n.2795-15022T>A		intron_variant, non_coding_transcript_variant
LOC105376481	XR_930796.3	n.904-15022T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658872.1	n.323-15022T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60976 AN: 151918 Hom.: 14214 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.401 AC: 60983 AN: 152036 Hom.: 14214 Cov.: 31 AF XY: 0.407 AC XY: 30221 AN XY: 74320

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.368

Alfa AF: 0.461 Hom.: 2187

Bravo AF: 0.378

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	2.1
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2793109; hg19: chr10-31379846;