rs10492467

Variant names:

• chr13-71167260-T-C
• rs10492467
• ENST00000428761.2:n.256-110T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-71167260-T-C
• chr13-71167260-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428761.2(LINC00348):​n.256-110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,992 control chromosomes in the GnomAD database, including 8,045 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 0.24 (8045 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00348 ENST00000428761.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 publications found

Genes affected

LINC00348 (HGNC:42658): (long intergenic non-protein coding RNA 348)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428761.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00348	NR_047699.1		n.160-110T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00348	ENST00000428761.2	TSL:3	n.256-110T>C		intron	N/A
	LINC00348	ENST00000653160.1		n.387-110T>C		intron	N/A
	LINC00348	ENST00000653878.1		n.282-110T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36280 AN: 151874 Hom.: 8016 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.239 AC: 36367 AN: 151992 Hom.: 8045 Cov.: 32 AF XY: 0.235 AC XY: 17427 AN XY: 74302

African (AFR) AF: 0.590 AC: 24433 AN: 41432

American (AMR) AF: 0.164 AC: 2499 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3464

East Asian (EAS) AF: 0.148 AC: 766 AN: 5168

South Asian (SAS) AF: 0.103 AC: 496 AN: 4816

European-Finnish (FIN) AF: 0.0618 AC: 654 AN: 10586

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0950 AC: 6458 AN: 67948

Other (OTH) AF: 0.205 AC: 432 AN: 2108

Alfa AF: 0.141 Hom.: 9609

Bravo AF: 0.262

Asia WGS AF: 0.162 AC: 564 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.29
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492467;

hg19: chr13-71741392;