chr5-175078380-G-C

Variant names:

• chr5-175078380-G-C
• rs11953281
• ENST00000798224.1:n.56+27916C>G

Variant summary

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

The ENST00000798224.1(LINC01951):​n.56+27916C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,030 control chromosomes in the GnomAD database, including 6,667 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 0.27 (6667 hom., cov: 33)
• Consequence: LINC01951 ENST00000798224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16
• Publications: 2 publications found

Genes affected

LINC01951 (HGNC:52774): (long intergenic non-protein coding RNA 1951)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01951	ENST00000798224.1	n.56+27916C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41357 AN: 151912 Hom.: 6650 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.272 AC: 41415 AN: 152030 Hom.: 6667 Cov.: 33 AF XY: 0.275 AC XY: 20411 AN XY: 74314

African (AFR) AF: 0.407 AC: 16889 AN: 41464

American (AMR) AF: 0.282 AC: 4302 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3466

East Asian (EAS) AF: 0.556 AC: 2871 AN: 5166

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1901 AN: 10578

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12388 AN: 67956

Other (OTH) AF: 0.260 AC: 550 AN: 2112

Alfa AF: 0.0964 Hom.: 103

Bravo AF: 0.289

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.061
DANN	Benign	0.37
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs11953281; hg19: chr5-174505383;