21-38344024-C-T

Position:

• chr21-38344024-C-T

Variant summary

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

The NR_110545.1(LINC01423):​n.182+1871G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,094 control chromosomes in the GnomAD database, including 1,259 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 0.12 (1259 hom., cov: 32)
• Consequence: LINC01423 NR_110545.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

Genes affected

LINC01423 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01423	NR_110545.1	n.182+1871G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18668 AN: 151976 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.123 AC: 18679 AN: 152094 Hom.: 1259 Cov.: 32 AF XY: 0.120 AC XY: 8922 AN XY: 74354

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.115

Alfa AF: 0.103 Hom.: 306

Bravo AF: 0.118

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836317; hg19: chr21-39715946;