rs4950322

Variant names:

• chr1-147383114-G-A
• rs4950322
• ENST00000621316.2:n.2454C>T

Variant summary

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

The ENST00000621316.2(LINC00624):​n.2454C>T 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 0.178 in 152,120 control chromosomes in the GnomAD database, including 2,592 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 0.18 (2592 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00624 ENST00000621316.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.2450C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000621316.2	n.2454C>T		non_coding_transcript_exon_variant	Exon 4 of 4	1
LINC00624	ENST00000619867.4	n.996+1554C>T		intron_variant	Intron 5 of 5	1
LINC00624	ENST00000803843.1	n.901-554C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27116 AN: 152002 Hom.: 2597 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.185

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.178 AC: 27109 AN: 152120 Hom.: 2592 Cov.: 32 AF XY: 0.177 AC XY: 13176 AN XY: 74366

African (AFR) AF: 0.133 AC: 5504 AN: 41520

American (AMR) AF: 0.183 AC: 2788 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3472

East Asian (EAS) AF: 0.0762 AC: 395 AN: 5182

South Asian (SAS) AF: 0.203 AC: 980 AN: 4828

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14162 AN: 67978

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.194 Hom.: 10002

Bravo AF: 0.170

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4950322; hg19: chr1-146854836;