rs10103840

Variant names:

• chr8-29562196-C-A
• rs10103840
• ENST00000798319.1:n.971G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000798319.1(ENSG00000303950):​n.971G>T variant causes a non coding transcript exon 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: ENSG00000303950 ENST00000798319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 2 publications found

Genes affected

ENSG00000303950 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798319.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303950	ENST00000798319.1		n.971G>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000303950	ENST00000798320.1		n.779G>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000303950	ENST00000798321.1		n.819G>T		non_coding_transcript_exon	Exon 4 of 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

African (AFR) AF: 0.206 AC: 8535 AN: 41458

American (AMR) AF: 0.147 AC: 2252 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3121 AN: 5166

South Asian (SAS) AF: 0.189 AC: 909 AN: 4806

European-Finnish (FIN) AF: 0.184 AC: 1944 AN: 10580

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8143 AN: 67958

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.165 Hom.: 998

Bravo AF: 0.175

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10103840; hg19: chr8-29419713;