2-67814710-T-G

Variant names:

• chr2-67814710-T-G
• rs7588898
• ENST00000457448.1:n.180+9164A>C

Variant summary

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

The ENST00000457448.1(LINC01812):​n.180+9164A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,898 control chromosomes in the GnomAD database, including 11,100 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 0.38 (11100 hom., cov: 32)
• Consequence: LINC01812 ENST00000457448.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

Genes affected

LINC01812 (HGNC:52616): (long intergenic non-protein coding RNA 1812)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01812	NR_110271.1	n.180+9164A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01812	ENST00000457448.1	n.180+9164A>C		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57660 AN: 151780 Hom.: 11086 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.380 AC: 57718 AN: 151898 Hom.: 11100 Cov.: 32 AF XY: 0.383 AC XY: 28411 AN XY: 74222

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.364

Alfa AF: 0.382 Hom.: 18310

Bravo AF: 0.394

Asia WGS AF: 0.410 AC: 1425 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7588898; hg19: chr2-68041842;