1-147430455-G-C

Variant names:

• chr1-147430455-G-C
• rs2353967
• ENST00000619867.4:n.701-21766C>G

Variant summary

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

The ENST00000619867.4(LINC00624):​n.701-21766C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,084 control chromosomes in the GnomAD database, including 39,453 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 0.71 (39453 hom., cov: 32)
• Consequence: LINC00624 ENST00000619867.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.701-45592C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.701-21766C>G		intron_variant	Intron 3 of 5	1
LINC00624	ENST00000621316.2	n.705-45592C>G		intron_variant	Intron 3 of 3	1
LINC00624	ENST00000803843.1	n.705-45592C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107846 AN: 151966 Hom.: 39381 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.710 AC: 107980 AN: 152084 Hom.: 39453 Cov.: 32 AF XY: 0.710 AC XY: 52807 AN XY: 74348

African (AFR) AF: 0.896 AC: 37193 AN: 41510

American (AMR) AF: 0.727 AC: 11117 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1725 AN: 3464

East Asian (EAS) AF: 0.602 AC: 3106 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4816

European-Finnish (FIN) AF: 0.684 AC: 7228 AN: 10562

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42405 AN: 67972

Other (OTH) AF: 0.669 AC: 1411 AN: 2108

Alfa AF: 0.562 Hom.: 1540

Bravo AF: 0.724

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2353967; hg19: chr1-146902186;