chr5-74373879-A-G

Variant names:

• chr5-74373879-A-G
• rs514878
• ENST00000507781.2:n.423-4358T>C

Variant summary

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

The ENST00000507781.2(LINC01331):​n.423-4358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,290 control chromosomes in the GnomAD database, including 68,395 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 0.95 (68395 hom., cov: 32)
• Consequence: LINC01331 ENST00000507781.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.36
• Publications: 0 publications found

Genes affected

LINC01331 (HGNC:50538): (long intergenic non-protein coding RNA 1331)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507781.2. 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
	LINC01331	NR_126354.2		n.220-4358T>C		intron	N/A
	LINC01331	NR_197435.1		n.105-4358T>C		intron	N/A
	LINC01331	NR_197436.1		n.257-4358T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01331	ENST00000507781.2	TSL:4	n.423-4358T>C		intron	N/A
	LINC01331	ENST00000663633.1		n.156-4358T>C		intron	N/A
	LINC01331	ENST00000715757.1		n.220-4358T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144103 AN: 152172 Hom.: 68329 Cov.: 32

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.947 AC: 144230 AN: 152290 Hom.: 68395 Cov.: 32 AF XY: 0.944 AC XY: 70297 AN XY: 74456

African (AFR) AF: 0.987 AC: 41011 AN: 41560

American (AMR) AF: 0.936 AC: 14328 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4468 AN: 5174

South Asian (SAS) AF: 0.860 AC: 4155 AN: 4830

European-Finnish (FIN) AF: 0.934 AC: 9916 AN: 10612

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63816 AN: 68026

Other (OTH) AF: 0.954 AC: 2012 AN: 2110

Alfa AF: 0.943 Hom.: 104927

Bravo AF: 0.951

Asia WGS AF: 0.844 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.23
PhyloP100		-4.4

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: rs514878;

hg19: chr5-73669704;