rs890995

Variant names:

• chr5-74492441-G-A
• rs890995
• ENST00000507781.2:n.308-15989C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-74492441-G-A
• chr5-74492441-G-C

Variant summary

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

The ENST00000507781.2(LINC01331):​n.308-15989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,852 control chromosomes in the GnomAD database, including 27,686 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 0.60 (27686 hom., cov: 30)
• Consequence: LINC01331 ENST00000507781.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01331	NR_126354.2	n.105-15989C>T		intron_variant	Intron 1 of 3
LINC01331	NR_197435.1	n.104+44229C>T		intron_variant	Intron 1 of 3
LINC01331	NR_197436.1	n.256+37969C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01331	ENST00000507781.2	n.308-15989C>T		intron_variant	Intron 1 of 5	4
LINC01331	ENST00000663633.1	n.155+44229C>T		intron_variant	Intron 1 of 2
LINC01331	ENST00000715757.1	n.105-15989C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91497 AN: 151734 Hom.: 27642 Cov.: 30

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.603 AC: 91590 AN: 151852 Hom.: 27686 Cov.: 30 AF XY: 0.604 AC XY: 44824 AN XY: 74196

African (AFR) AF: 0.601 AC: 24852 AN: 41384

American (AMR) AF: 0.669 AC: 10193 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2650 AN: 5148

South Asian (SAS) AF: 0.633 AC: 3045 AN: 4808

European-Finnish (FIN) AF: 0.562 AC: 5924 AN: 10550

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40614 AN: 67946

Other (OTH) AF: 0.602 AC: 1263 AN: 2098

Alfa AF: 0.601 Hom.: 114989

Bravo AF: 0.610

Asia WGS AF: 0.580 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.26
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs890995; hg19: chr5-73788266;