rs10091038

Variant names:

• chr8-29502788-A-C
• rs10091038
• ENST00000798110.1:n.68+8490A>C

Variant summary

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

The ENST00000798110.1(LINC02948):​n.68+8490A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,992 control chromosomes in the GnomAD database, including 25,345 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 0.57 (25345 hom., cov: 31)
• Consequence: LINC02948 ENST00000798110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 19 publications found

Genes affected

LINC02948 (HGNC:55963): (long intergenic non-protein coding RNA 2948)

ENSG00000253632 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02948	ENST00000798110.1	n.68+8490A>C		intron_variant	Intron 1 of 3
ENSG00000253632	ENST00000798477.1	n.49+6712A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87044 AN: 151874 Hom.: 25320 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.573 AC: 87116 AN: 151992 Hom.: 25345 Cov.: 31 AF XY: 0.577 AC XY: 42866 AN XY: 74290

African (AFR) AF: 0.550 AC: 22805 AN: 41450

American (AMR) AF: 0.553 AC: 8443 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3996 AN: 5170

South Asian (SAS) AF: 0.674 AC: 3250 AN: 4820

European-Finnish (FIN) AF: 0.650 AC: 6852 AN: 10546

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38221 AN: 67952

Other (OTH) AF: 0.561 AC: 1186 AN: 2114

Alfa AF: 0.564 Hom.: 105619

Bravo AF: 0.559

Asia WGS AF: 0.699 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10091038; hg19: chr8-29360305;