rs7421966

Variant names:

• chr2-22745650-G-A
• rs7421966
• ENST00000833264.1:n.86+3519C>T

Variant summary

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

The ENST00000833264.1(LINC01830):​n.86+3519C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,964 control chromosomes in the GnomAD database, including 18,156 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 0.48 (18156 hom., cov: 32)
• Consequence: LINC01830 ENST00000833264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 1 publications found

Genes affected

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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
LINC01830	ENST00000833264.1	n.86+3519C>T		intron_variant	Intron 1 of 5
LINC01830	ENST00000833265.1	n.108+3519C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72528 AN: 151846 Hom.: 18150 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.477 AC: 72556 AN: 151964 Hom.: 18156 Cov.: 32 AF XY: 0.473 AC XY: 35128 AN XY: 74270

African (AFR) AF: 0.351 AC: 14547 AN: 41440

American (AMR) AF: 0.465 AC: 7093 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1192 AN: 5168

South Asian (SAS) AF: 0.482 AC: 2324 AN: 4818

European-Finnish (FIN) AF: 0.501 AC: 5283 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38436 AN: 67936

Other (OTH) AF: 0.509 AC: 1077 AN: 2114

Alfa AF: 0.549 Hom.: 16847

Bravo AF: 0.470

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.74
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7421966; hg19: chr2-22968522;