5-61675951-G-T

Variant names:

• chr5-61675951-G-T
• rs410850
• ENST00000505623.5:n.124+1672C>A

Variant summary

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

The ENST00000505623.5(ENSG00000248529):​n.124+1672C>A 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: ENSG00000248529 ENST00000505623.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 3 publications found

Genes affected

ENSG00000248529 (HGNC:58412):

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03152	NR_109910.1	n.1161+1672C>A		intron_variant	Intron 6 of 7
LINC03122	NR_126523.1	n.141-27915G>T		intron_variant	Intron 2 of 2
LINC03122	NR_126524.1	n.141-27915G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248529	ENST00000505623.5	n.124+1672C>A		intron_variant	Intron 2 of 4	1
ENSG00000248529	ENST00000507264.6	n.178+1672C>A		intron_variant	Intron 2 of 2	1
ENSG00000248529	ENST00000513386.1	n.1161+1672C>A		intron_variant	Intron 6 of 7	1

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

Alfa AF: 0.00 Hom.: 15072

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0040
DANN	Benign	0.74
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs410850; hg19: chr5-60971778;