5-74188595-G-T

Variant names:

• chr5-74188595-G-T
• rs16871467
• ENST00000663633.1:n.324-75444C>A

Variant summary

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

The ENST00000663633.1(LINC01331):​n.324-75444C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 152,190 control chromosomes in the GnomAD database, including 192 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 0.034 (192 hom., cov: 32)
• Consequence: LINC01331 ENST00000663633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663633.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01331	ENST00000663633.1		n.324-75444C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5172 AN: 152072 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0341 AC: 5183 AN: 152190 Hom.: 192 Cov.: 32 AF XY: 0.0340 AC XY: 2533 AN XY: 74418

African (AFR) AF: 0.0836 AC: 3473 AN: 41522

American (AMR) AF: 0.0178 AC: 273 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3462

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5180

South Asian (SAS) AF: 0.0892 AC: 429 AN: 4812

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 732 AN: 67998

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0207 Hom.: 38

Bravo AF: 0.0361

Asia WGS AF: 0.0660 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.47
DANN	Benign	0.74
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs16871467; hg19: chr5-73484420;