chr1-147431348-G-T

Variant names:

• chr1-147431348-G-T
• rs12728058
• ENST00000619867.4:n.701-22659C>A

Variant summary

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

The ENST00000619867.4(LINC00624):​n.701-22659C>A variant causes a intron 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 ENST00000619867.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619867.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	NR_038423.2		n.701-46485C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	ENST00000619867.4	TSL:1	n.701-22659C>A		intron	N/A
	LINC00624	ENST00000621316.2	TSL:1	n.705-46485C>A		intron	N/A
	LINC00624	ENST00000803843.1		n.705-46485C>A		intron	N/A

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

African (AFR) AF: 0.940 AC: 38848 AN: 41320

American (AMR) AF: 0.754 AC: 11455 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1917 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3095 AN: 5104

South Asian (SAS) AF: 0.643 AC: 3080 AN: 4790

European-Finnish (FIN) AF: 0.710 AC: 7264 AN: 10230

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44746 AN: 67762

Other (OTH) AF: 0.709 AC: 1486 AN: 2096

Alfa AF: 0.682 Hom.: 12019

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.072
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12728058;