ENST00000565815.1:n.2464A>C

Variant names:

• chr13-75932669-T-G
• rs7317138
• ENST00000565815.1:n.2464A>C

Variant summary

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

The ENST00000565815.1(LINC00561):​n.2464A>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 0.15 in 152,108 control chromosomes in the GnomAD database, including 1,818 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 0.15 (1818 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LINC00561 ENST00000565815.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 1 publications found

Genes affected

LINC00561 (HGNC:43705): (long intergenic non-protein coding RNA 561)

ENSG00000309105 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565815.1. 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
	LINC00561	NR_047491.1		n.2464A>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00561	ENST00000565815.1	TSL:6	n.2464A>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309105	ENST00000838613.1		n.51-2066T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22845 AN: 151974 Hom.: 1818 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0625 AC: 1 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.150 AC: 22862 AN: 152092 Hom.: 1818 Cov.: 32 AF XY: 0.149 AC XY: 11111 AN XY: 74346

African (AFR) AF: 0.159 AC: 6590 AN: 41510

American (AMR) AF: 0.210 AC: 3195 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 208 AN: 3468

East Asian (EAS) AF: 0.138 AC: 712 AN: 5166

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4818

European-Finnish (FIN) AF: 0.151 AC: 1605 AN: 10598

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9749 AN: 67964

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.144 Hom.: 2878

Bravo AF: 0.157

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.55
PhyloP100		0.29

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: rs7317138;

hg19: chr13-76506805;