rs10951138

Variant names:

• chr7-26442184-G-A
• rs10951138
• ENST00000421862.2:n.557+1679G>A

Variant summary

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

The ENST00000421862.2(LINC02981):​n.557+1679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,134 control chromosomes in the GnomAD database, including 5,234 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 0.25 (5234 hom., cov: 33)
• Consequence: LINC02981 ENST00000421862.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 7 publications found

Genes affected

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

ENSG00000299146 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02981	NR_148499.1	n.630+29945G>A		intron_variant	Intron 3 of 6
LINC02981	NR_148500.1	n.225+29945G>A		intron_variant	Intron 2 of 5
LINC02981	NR_148501.1	n.508+29945G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02981	ENST00000421862.2	n.557+1679G>A		intron_variant	Intron 2 of 2	5
LINC02981	ENST00000430548.5	n.422-37684G>A		intron_variant	Intron 1 of 1	4
LINC02981	ENST00000439120.2	n.429+43163G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37377 AN: 152016 Hom.: 5235 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.246 AC: 37392 AN: 152134 Hom.: 5234 Cov.: 33 AF XY: 0.247 AC XY: 18399 AN XY: 74390

African (AFR) AF: 0.373 AC: 15460 AN: 41476

American (AMR) AF: 0.174 AC: 2662 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2447 AN: 5180

South Asian (SAS) AF: 0.187 AC: 902 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10582

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12314 AN: 68008

Other (OTH) AF: 0.229 AC: 485 AN: 2114

Alfa AF: 0.206 Hom.: 14339

Bravo AF: 0.251

Asia WGS AF: 0.307 AC: 1069 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	0.34
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10951138; hg19: chr7-26481804;