rs2776601

Variant names:

• chr14-97973143-C-A
• rs2776601
• ENST00000499006.8:n.161-3596G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-97973143-C-A
• chr14-97973143-C-G
• chr14-97973143-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000736874.1(LINC01550):​n.247G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LINC01550 ENST00000736874.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 3 publications found

Genes affected

LINC01550 (HGNC:20111): (long intergenic non-protein coding RNA 1550)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736874.1. 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
	LINC01550	NR_015430.2		n.149-3596G>T		intron	N/A
	LINC01550	NR_152746.1		n.149-3596G>T		intron	N/A
	LINC01550	NR_152747.1		n.149-3596G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01550	ENST00000499006.8	TSL:1	n.161-3596G>T		intron	N/A
	LINC01550	ENST00000512901.6	TSL:1	n.133-3596G>T		intron	N/A
	LINC01550	ENST00000736874.1		n.247G>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.35
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2776601; hg19: chr14-98439480;