rs10496166

Variant names:

• chr2-68836777-G-A
• rs10496166
• ENST00000415448.1:n.416C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-68836777-G-A
• chr2-68836777-G-C
• chr2-68836777-G-T

Variant summary

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

The ENST00000415448.1(LINC01890):​n.416C>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 0.249 in 152,126 control chromosomes in the GnomAD database, including 5,746 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 0.25 (5746 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01890 ENST00000415448.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 12 publications found

Genes affected

LINC01890 (HGNC:52709): (long intergenic non-protein coding RNA 1890)

LINC01888 (HGNC:52707): (long intergenic non-protein coding RNA 1888)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01890	NR_183884.1	n.431C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LINC01890	NR_183885.1	n.431C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LINC01890	NR_183886.1	n.431C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01890	ENST00000415448.1	n.416C>T		non_coding_transcript_exon_variant	Exon 1 of 2	2
LINC01890	ENST00000652076.1	n.449C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01890	ENST00000653356.1	n.459C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37800 AN: 152008 Hom.: 5728 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.249 AC: 37868 AN: 152126 Hom.: 5746 Cov.: 32 AF XY: 0.250 AC XY: 18614 AN XY: 74360

African (AFR) AF: 0.402 AC: 16667 AN: 41468

American (AMR) AF: 0.279 AC: 4272 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2231 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1695 AN: 10574

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10473 AN: 68010

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.191 Hom.: 11888

Bravo AF: 0.265

Asia WGS AF: 0.348 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.29
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10496166; hg19: chr2-69063909;