rs1320561

Variant names:

• chr20-23117243-G-A
• rs1320561
• ENST00000762248.1:n.161C>T

Variant summary

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

The ENST00000762248.1(LINC00656):​n.161C>T 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 0.514 in 152,072 control chromosomes in the GnomAD database, including 21,078 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 0.51 (21078 hom., cov: 33)
• Consequence: LINC00656 ENST00000762248.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 10 publications found

Genes affected

LINC00656 (HGNC:27304): (long intergenic non-protein coding RNA 656)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762248.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00656	ENST00000762248.1		n.161C>T		non_coding_transcript_exon	Exon 1 of 3
	LINC00656	ENST00000762249.1		n.144C>T		non_coding_transcript_exon	Exon 1 of 2
	LINC00656	ENST00000762250.1		n.127C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78139 AN: 151954 Hom.: 21063 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.514 AC: 78170 AN: 152072 Hom.: 21078 Cov.: 33 AF XY: 0.506 AC XY: 37632 AN XY: 74328

African (AFR) AF: 0.363 AC: 15037 AN: 41476

American (AMR) AF: 0.592 AC: 9044 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2741 AN: 5156

South Asian (SAS) AF: 0.588 AC: 2839 AN: 4828

European-Finnish (FIN) AF: 0.409 AC: 4318 AN: 10566

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40062 AN: 67978

Other (OTH) AF: 0.565 AC: 1192 AN: 2108

Alfa AF: 0.568 Hom.: 100230

Bravo AF: 0.522

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.57
PhyloP100		-0.99

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: rs1320561;

hg19: chr20-23097880;