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 ENST00000499006.8(LINC01550):​n.161-3596G>T variant causes a intron 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 ENST00000499006.8 intron
• 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01550	NR_015430.2	n.149-3596G>T		intron_variant	Intron 1 of 2
LINC01550	NR_152746.1	n.149-3596G>T		intron_variant	Intron 1 of 3
LINC01550	NR_152747.1	n.149-3596G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01550	ENST00000499006.8	n.161-3596G>T		intron_variant	Intron 1 of 2	1
LINC01550	ENST00000512901.6	n.133-3596G>T		intron_variant	Intron 1 of 2	1
LINC01550	ENST00000736874.1	n.247G>T		non_coding_transcript_exon_variant	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 v4.3

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;