rs638080

Variant names:

• chr19-23409406-G-C
• rs638080
• ENST00000600643.6:n.252-4071C>G

Variant summary

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

The ENST00000600643.6(LINC01224):​n.252-4071C>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 ENST00000600643.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

Genes affected

LINC01224 (HGNC:49676): (long intergenic non-protein coding RNA 1224)

ENSG00000306337 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01224	NR_126448.1	n.182-4071C>G		intron_variant	Intron 1 of 5
LINC01224	NR_126449.1	n.182-4071C>G		intron_variant	Intron 1 of 4
LOC105372335	XR_007067208.1	n.103-2671G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01224	ENST00000600643.6	n.252-4071C>G		intron_variant	Intron 1 of 4	1
LINC01224	ENST00000593573.6	n.294-4071C>G		intron_variant	Intron 1 of 5	4
LINC01224	ENST00000594576.6	n.241-4071C>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.516 AC: 20830 AN: 40366

American (AMR) AF: 0.199 AC: 3018 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1006 AN: 3462

East Asian (EAS) AF: 0.146 AC: 747 AN: 5132

South Asian (SAS) AF: 0.237 AC: 1129 AN: 4762

European-Finnish (FIN) AF: 0.241 AC: 2455 AN: 10196

Middle Eastern (MID) AF: 0.269 AC: 77 AN: 286

European-Non Finnish (NFE) AF: 0.263 AC: 17753 AN: 67508

Other (OTH) AF: 0.293 AC: 611 AN: 2084

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs638080; hg19: chr19-23592208;