rs959931

Variant names:

• chr5-159843706-C-T
• rs959931
• ENST00000522627.1:n.3691+23166G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522627.1(LINC01847):​n.3691+23166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,038 control chromosomes in the GnomAD database, including 5,174 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 0.25 (5174 hom., cov: 32)
• Consequence: LINC01847 ENST00000522627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01847	NR_109891.1	n.3691+23166G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01847	ENST00000522627.1	n.3691+23166G>A		intron_variant	Intron 2 of 2	1
LINC01847	ENST00000641163.1	n.252+24152G>A		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37690 AN: 151920 Hom.: 5162 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.248 AC: 37739 AN: 152038 Hom.: 5174 Cov.: 32 AF XY: 0.251 AC XY: 18621 AN XY: 74302

African (AFR) AF: 0.380 AC: 15749 AN: 41452

American (AMR) AF: 0.160 AC: 2444 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.158 AC: 816 AN: 5168

South Asian (SAS) AF: 0.206 AC: 991 AN: 4806

European-Finnish (FIN) AF: 0.252 AC: 2663 AN: 10552

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13775 AN: 67984

Other (OTH) AF: 0.228 AC: 480 AN: 2108

Alfa AF: 0.214 Hom.: 13891

Bravo AF: 0.246

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs959931; hg19: chr5-159270713;