rs1595781

Variant names:

• chr3-165337681-C-A
• rs1595781
• ENST00000470138.5:n.201-45114C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-165337681-C-A
• chr3-165337681-C-G
• chr3-165337681-C-T

Variant summary

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

The ENST00000470138.5(LINC01322):​n.201-45114C>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: 33)
• Consequence: LINC01322 ENST00000470138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 3 publications found

Genes affected

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01322	NR_125764.2	n.213-36578C>A		intron_variant	Intron 1 of 5
LINC01322	NR_174098.1	n.213-7791C>A		intron_variant	Intron 1 of 6
LINC01322	NR_174099.1	n.213-7791C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01322	ENST00000470138.5	n.201-45114C>A		intron_variant	Intron 1 of 3	4
LINC01322	ENST00000494915.2	n.165-7791C>A		intron_variant	Intron 1 of 4	4
LINC01322	ENST00000498616.7	n.203-7791C>A		intron_variant	Intron 1 of 6	4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 13825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.61
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1595781; hg19: chr3-165055469;