rs4743820

Variant names:

• chr9-91166134-C-A
• rs4743820
• ENST00000659376.2:n.3885C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-91166134-C-A
• chr9-91166134-C-G
• chr9-91166134-C-T

Variant summary

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

The ENST00000659376.2(LINC00484):​n.3885C>A 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: 30)
• Consequence: LINC00484 ENST00000659376.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 46 publications found

Genes affected

LINC00484 (HGNC:27862): (long intergenic non-protein coding RNA 484)

LINC02937 (HGNC:55942): (long intergenic non-protein coding RNA 2937)

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
LINC00484	NR_135306.1	n.161-16335C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00484	ENST00000659376.2	n.3885C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00484	ENST00000439438.1	n.161-16335C>A		intron_variant	Intron 2 of 2	3
LINC02937	ENST00000667274.1	n.202+46711G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.69
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs4743820; hg19: chr9-93928416;