rs31685

chr5-159857166-G-Achr5-159857166-G-Cchr5-159857166-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109891.1(LINC01847):n.3691+9706C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,124 control chromosomes in the GnomAD database, including 43,991 homozygotes. 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: 𝑓 0.75 (43991 hom., cov: 32)
• Consequence: LINC01847 NR_109891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

LINC01847 (HGNC:52662): (long intergenic non-protein coding RNA 1847)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01847	NR_109891.1	n.3691+9706C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01847	ENST00000522627.1	n.3691+9706C>T		intron_variant, non_coding_transcript_variant		1
LINC01847	ENST00000641163.1	n.252+10692C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114089 AN: 152006 Hom.: 43930 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.751 AC: 114205 AN: 152124 Hom.: 43991 Cov.: 32 AF XY: 0.749 AC XY: 55723 AN XY: 74378

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.746

Alfa AF: 0.714 Hom.: 6352

Bravo AF: 0.765

Asia WGS AF: 0.807 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.98
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31685; hg19: chr5-159284173;