rs11783570

Variant names:

• chr8-66192136-T-C
• rs11783570
• ENST00000517725.2:n.47T>C

Variant summary

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

The ENST00000517725.2(LINC00967):​n.47T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,444 control chromosomes in the GnomAD database, including 205 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 0.043 (205 hom., cov: 32)
  • Exomes 𝑓: 0.051 (0 hom.)
• Consequence: LINC00967 ENST00000517725.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 1 publications found

Genes affected

LINC00967 (HGNC:48725): (long intergenic non-protein coding RNA 967)

ENSG00000295392 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517725.2. 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
	LINC00967	NR_039979.1		n.23T>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00967	ENST00000517725.2	TSL:2	n.47T>C		non_coding_transcript_exon	Exon 1 of 5
	LINC00967	ENST00000518035.6	TSL:2	n.136T>C		non_coding_transcript_exon	Exon 1 of 3
	LINC00967	ENST00000518412.1	TSL:5	n.44T>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0435 AC: 6616 AN: 152208 Hom.: 205 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0478

GnomAD4 exome AF: 0.0508 AC: 6 AN: 118 Hom.: 0 Cov.: 0 AF XY: 0.0581 AC XY: 5 AN XY: 86

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0568 AC: 5 AN: 88

Other (OTH) AF: 0.00 AC: 0 AN: 12

GnomAD4 genome AF: 0.0434 AC: 6613 AN: 152326 Hom.: 205 Cov.: 32 AF XY: 0.0438 AC XY: 3261 AN XY: 74480

African (AFR) AF: 0.0120 AC: 500 AN: 41584

American (AMR) AF: 0.0337 AC: 516 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0650 AC: 314 AN: 4830

European-Finnish (FIN) AF: 0.0734 AC: 780 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0617 AC: 4197 AN: 68020

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0528 Hom.: 57

Bravo AF: 0.0386

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.66
PhyloP100		-3.0

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: rs11783570;

hg19: chr8-67104371;