rs7729084

Variant names:

• chr5-174954577-A-C
• rs7729084
• ENST00000377300.4:n.1281+21872T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-174954577-A-C
• chr5-174954577-A-T

Variant summary

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

The ENST00000377300.4(LINC01951):​n.1281+21872T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,176 control chromosomes in the GnomAD database, including 9,455 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 0.22 (9455 hom., cov: 33)
• Consequence: LINC01951 ENST00000377300.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377300.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01951	NR_046113.1		n.1499+21872T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01951	ENST00000377300.4	TSL:2	n.1281+21872T>G		intron	N/A
	LINC01951	ENST00000798224.1		n.265+21872T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33900 AN: 152058 Hom.: 9400 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.224 AC: 34017 AN: 152176 Hom.: 9455 Cov.: 33 AF XY: 0.216 AC XY: 16039 AN XY: 74410

African (AFR) AF: 0.660 AC: 27352 AN: 41442

American (AMR) AF: 0.117 AC: 1794 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3470

East Asian (EAS) AF: 0.0379 AC: 197 AN: 5196

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4826

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3391 AN: 68024

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.0726 Hom.: 803

Bravo AF: 0.249

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.057
DANN	Benign	0.71
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7729084;

hg19: chr5-174381580;