chr1-147431348-G-T

Position:

• chr1-147431348-G-T

Variant summary

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

The NR_038423.2(LINC00624):​n.701-46485C>A 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 0.746 in 151,168 control chromosomes in the GnomAD database, including 43,221 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 0.75 (43221 hom., cov: 28)
• Consequence: LINC00624 NR_038423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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 (Cadd=0.072).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.701-46485C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.701-22659C>A		intron_variant, non_coding_transcript_variant		1
LINC00624	ENST00000621316.1	n.701-46485C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 112600 AN: 151058 Hom.: 43151 Cov.: 28

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.746 AC: 112727 AN: 151168 Hom.: 43221 Cov.: 28 AF XY: 0.745 AC XY: 54903 AN XY: 73724

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.709

Alfa AF: 0.664 Hom.: 6471

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.072

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12728058; hg19: -;