chr1-147517855-G-C

Position:

• chr1-147517855-G-C

Variant summary

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

The NR_038423.2(LINC00624):​n.21C>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 0.992 in 152,386 control chromosomes in the GnomAD database, including 74,909 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 0.99 (74885 hom., cov: 32)
  • Exomes 𝑓: 1.0 (24 hom.)
• Consequence: LINC00624 NR_038423.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.21C>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.21C>G		non_coding_transcript_exon_variant	1/6	1
LINC00624	ENST00000621316.1	n.21C>G		non_coding_transcript_exon_variant	1/4	1

Frequencies

GnomAD3 genomes AF: 0.992 AC: 150933 AN: 152220 Hom.: 74827 Cov.: 32

Gnomad AFR AF: 0.988

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.998

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.990

GnomAD4 exome AF: 1.00 AC: 48 AN: 48 Hom.: 24 Cov.: 0 AF XY: 1.00 AC XY: 34 AN XY: 34

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.992 AC: 151050 AN: 152338 Hom.: 74885 Cov.: 32 AF XY: 0.992 AC XY: 73886 AN XY: 74494

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.993

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.991

Alfa AF: 0.990 Hom.: 3443

Bravo AF: 0.991

Asia WGS AF: 0.999 AC: 3473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs681814; hg19: chr1-146989679;