7-26435254-T-C

Variant names:

• chr7-26435254-T-C
• rs10238880
• ENST00000421862.2:n.422-5116T>C

Variant summary

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

The ENST00000421862.2(LINC02981):​n.422-5116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,132 control chromosomes in the GnomAD database, including 4,035 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 (4035 hom., cov: 32)
• Consequence: LINC02981 ENST00000421862.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 4 publications found

Genes affected

LINC02981 (HGNC:56055): (long intergenic non-protein coding RNA 2981)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02981	NR_148499.1	n.630+23015T>C		intron_variant	Intron 3 of 6
LINC02981	NR_148500.1	n.225+23015T>C		intron_variant	Intron 2 of 5
LINC02981	NR_148501.1	n.508+23015T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02981	ENST00000421862.2	n.422-5116T>C		intron_variant	Intron 1 of 2	5
LINC02981	ENST00000430548.5	n.421+36233T>C		intron_variant	Intron 1 of 1	4
LINC02981	ENST00000439120.2	n.429+36233T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33827 AN: 152016 Hom.: 4026 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.223 AC: 33874 AN: 152132 Hom.: 4035 Cov.: 32 AF XY: 0.225 AC XY: 16767 AN XY: 74374

African (AFR) AF: 0.285 AC: 11842 AN: 41490

American (AMR) AF: 0.234 AC: 3582 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 550 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1770 AN: 5164

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2576 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11918 AN: 68002

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.186 Hom.: 4774

Bravo AF: 0.227

Asia WGS AF: 0.308 AC: 1072 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10238880; hg19: chr7-26474874;