rs638080

Positions:

• chr19-23409406-G-C

Variant summary

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

The ENST00000600643.5(LINC01224):​n.179-4071C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 149,838 control chromosomes in the GnomAD database, including 8,849 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 0.32 (8849 hom., cov: 28)
• Consequence: LINC01224 ENST00000600643.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

LINC01224 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01224	NR_126448.1	n.182-4071C>G		intron_variant
LINC01224	NR_126449.1	n.182-4071C>G		intron_variant
LOC105372335	XR_007067208.1	n.103-2671G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01224	ENST00000600643.5	n.179-4071C>G		intron_variant		1
LINC01224	ENST00000593573.5	n.167-4071C>G		intron_variant		4
LINC01224	ENST00000594576.5	n.163-4071C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.319 AC: 47791 AN: 149734 Hom.: 8810 Cov.: 28

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.319 AC: 47869 AN: 149838 Hom.: 8849 Cov.: 28 AF XY: 0.314 AC XY: 22948 AN XY: 73096

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.293

Alfa AF: 0.298 Hom.: 947

Bravo AF: 0.329

Asia WGS AF: 0.199 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638080; hg19: chr19-23592208;