rs9362054

Positions:

• chr6-84468550-T-A
• chr6-84468550-T-C

Variant summary

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

The NR_132100.1(LINC01611):​n.217+2241A>T variant causes a intron, non coding transcript 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: 31)
• Consequence: LINC01611 NR_132100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

LINC01611 (HGNC:51791): (long intergenic non-protein coding RNA 1611)

LOC107986620 (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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01611	NR_132100.1	n.217+2241A>T		intron_variant, non_coding_transcript_variant
LOC107986620	XR_001744235.2	n.191+15223T>A		intron_variant, non_coding_transcript_variant
LOC107986620	XR_001744236.1	n.134+15223T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01611	ENST00000454172.5	n.135-24099A>T		intron_variant, non_coding_transcript_variant		3
LINC01611	ENST00000428896.1	n.217+2241A>T		intron_variant, non_coding_transcript_variant		5
LINC01611	ENST00000454981.5	n.114+2241A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9362054; hg19: chr6-85178268;