4-185078389-G-C

Variant names:

• chr4-185078389-G-C
• rs6841061
• ENST00000509017.6:n.1499+6316G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_939565.3(LOC105377588):​n.1236C>G 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: 33)
• Consequence: LOC105377588 XR_939565.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

LINC02436 (HGNC:53368): (long intergenic non-protein coding RNA 2436)

LOC105377588 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377588	XR_002959837.1	n.890C>G		non_coding_transcript_exon_variant	Exon 2 of 3
LOC105377588	XR_939565.3	n.1236C>G		non_coding_transcript_exon_variant	Exon 4 of 5
LINC02436	NR_147059.2	n.1359+6316G>C		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02436	ENST00000509017.6	n.1499+6316G>C		intron_variant	Intron 6 of 9	1
LINC02436	ENST00000652785.1	n.394-7395G>C		intron_variant	Intron 3 of 5
LINC02436	ENST00000653662.1	n.691+6669G>C		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.38
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6841061; hg19: chr4-185999543;