rs17412858

chr13-109600261-A-G

Variant summary

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

The ENST00000650264.1(ENSG00000285534):n.759-29103T>C 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 0.276 in 152,082 control chromosomes in the GnomAD database, including 6,895 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 0.28 (6895 hom., cov: 32)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.940+5948T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-29103T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41967 AN: 151964 Hom.: 6893 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.276 AC: 41967 AN: 152082 Hom.: 6895 Cov.: 32 AF XY: 0.273 AC XY: 20269 AN XY: 74334

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.284

Alfa AF: 0.328 Hom.: 2470

Bravo AF: 0.266

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.25
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17412858; hg19: chr13-110252608;