rs2000072

chr1-147498757-A-Gchr1-147498757-A-T

Variant summary

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

The NR_038423.2(LINC00624):n.700+15581T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,160 control chromosomes in the GnomAD database, including 55,459 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 0.85 (55459 hom., cov: 30)
• Consequence: LINC00624 NR_038423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00624	NR_038423.2	n.700+15581T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00624	ENST00000619867.4	n.700+15581T>C		intron_variant, non_coding_transcript_variant		1
LINC00624	ENST00000621316.1	n.700+15581T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129076 AN: 152042 Hom.: 55387 Cov.: 30

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.849 AC: 129205 AN: 152160 Hom.: 55459 Cov.: 30 AF XY: 0.852 AC XY: 63338 AN XY: 74370

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.824

Alfa AF: 0.802 Hom.: 24441

Bravo AF: 0.857

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2000072; hg19: chr1-146970568;