rs2353969

Variant names:

• chr1-147421827-G-C
• rs2353969
• ENST00000619867.4:n.701-13138C>G

Variant summary

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

The ENST00000619867.4(LINC00624):​n.701-13138C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,996 control chromosomes in the GnomAD database, including 39,259 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 0.71 (39259 hom., cov: 31)
• Consequence: LINC00624 ENST00000619867.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

Genes affected

LINC00624 (HGNC:44254): (long intergenic non-protein coding RNA 624)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.701-36964C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.701-13138C>G		intron_variant	Intron 3 of 5	1
LINC00624	ENST00000621316.1	n.701-36964C>G		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107559 AN: 151878 Hom.: 39189 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.709 AC: 107691 AN: 151996 Hom.: 39259 Cov.: 31 AF XY: 0.709 AC XY: 52630 AN XY: 74262

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.668

Alfa AF: 0.687 Hom.: 4564

Bravo AF: 0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353969; hg19: chr1-146893554;