rs10169728

Variant names:

• chr2-65778497-A-C
• rs10169728
• ENST00000606978.5:n.668+23714A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-65778497-A-C
• chr2-65778497-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.668+23714A>C		intron_variant	Intron 6 of 9	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;