rs10103840

Variant names:

• chr8-29562196-C-A
• rs10103840
• ENST00000522028.1:n.244-1825C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-29562196-C-A
• chr8-29562196-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522028.1(LINC02948):​n.244-1825C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,040 control chromosomes in the GnomAD database, including 2,834 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 0.17 (2834 hom., cov: 32)
• Consequence: LINC02948 ENST00000522028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02948	XR_001745861.2	n.-77C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02948	ENST00000522028.1	n.244-1825C>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25788 AN: 151920 Hom.: 2829 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.170 AC: 25828 AN: 152040 Hom.: 2834 Cov.: 32 AF XY: 0.175 AC XY: 13016 AN XY: 74312

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.164

Alfa AF: 0.151 Hom.: 356

Bravo AF: 0.175

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10103840; hg19: chr8-29419713;