chr2-161248273-C-G

Variant names:

• chr2-161248273-C-G
• rs1146030
• ENST00000436506.5:n.1700C>G

Variant summary

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

The ENST00000436506.5(LINC01806):​n.1700C>G 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 0.907 in 152,208 control chromosomes in the GnomAD database, including 62,664 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 0.91 (62664 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC01806 ENST00000436506.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 2 publications found

Genes affected

LINC01806 (HGNC:52599): (long intergenic non-protein coding RNA 1806)

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01806	NR_110163.1	n.1600C>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01806	NR_110164.1	n.1556C>G		non_coding_transcript_exon_variant	Exon 2 of 2
PSMD14-DT	NR_110593.1	n.348+251G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01806	ENST00000436506.5	n.1700C>G		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC01806	ENST00000439050.2	n.1576C>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC01806	ENST00000655684.3	n.1622C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137981 AN: 152090 Hom.: 62611 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.890

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.907 AC: 138094 AN: 152208 Hom.: 62664 Cov.: 33 AF XY: 0.907 AC XY: 67519 AN XY: 74408

African (AFR) AF: 0.929 AC: 38602 AN: 41562

American (AMR) AF: 0.916 AC: 14002 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5180 AN: 5190

South Asian (SAS) AF: 0.893 AC: 4313 AN: 4828

European-Finnish (FIN) AF: 0.886 AC: 9392 AN: 10598

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60591 AN: 67956

Other (OTH) AF: 0.891 AC: 1880 AN: 2110

Alfa AF: 0.894 Hom.: 2885

Bravo AF: 0.914

Asia WGS AF: 0.938 AC: 3250 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.30
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1146030; hg19: chr2-162104784;