chr1-147498757-A-G

Variant names:

• chr1-147498757-A-G
• rs2000072
• ENST00000619867.4:n.700+15581T>C

Variant summary

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

The ENST00000619867.4(LINC00624):​n.700+15581T>C variant causes a intron 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 ENST00000619867.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• 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 (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.700+15581T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00624	ENST00000619867.4	TSL:1	n.700+15581T>C		intron	N/A
	LINC00624	ENST00000621316.2	TSL:1	n.704+15581T>C		intron	N/A
	LINC00624	ENST00000803843.1		n.704+15581T>C		intron	N/A

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

African (AFR) AF: 0.962 AC: 39948 AN: 41538

American (AMR) AF: 0.860 AC: 13146 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2466 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5180

South Asian (SAS) AF: 0.928 AC: 4455 AN: 4802

European-Finnish (FIN) AF: 0.809 AC: 8551 AN: 10572

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52665 AN: 67998

Other (OTH) AF: 0.824 AC: 1739 AN: 2110

Alfa AF: 0.799 Hom.: 26808

Bravo AF: 0.857

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.36
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2000072; hg19: chr1-146970568;