rs10169728

chr2-65778497-A-Cchr2-65778497-A-T

Variant summary

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

The ENST00000606978.5(LINC02934):n.668+23714A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,094 control chromosomes in the GnomAD database, including 3,880 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 0.18 (3880 hom., cov: 33)
• Consequence: LINC02934 ENST00000606978.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02934	ENST00000606978.5	n.668+23714A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26770 AN: 151976 Hom.: 3871 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.176 AC: 26827 AN: 152094 Hom.: 3880 Cov.: 33 AF XY: 0.178 AC XY: 13242 AN XY: 74366

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0615 Hom.: 147

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169728; hg19: chr2-66005631;