22-34137753-C-T

Position:

• chr22-34137753-C-T

Variant summary

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

The NR_183585.1(LINC01643):​n.400-23843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,148 control chromosomes in the GnomAD database, including 54,697 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 0.84 (54697 hom., cov: 31)
• Consequence: LINC01643 NR_183585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

LINC01643 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01643	NR_183585.1	n.400-23843C>T		intron_variant
LINC01643	NR_183586.1	n.240-23843C>T		intron_variant
LINC01643	NR_183587.1	n.348+28319C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01643	ENST00000412218.1	n.199-14112C>T		intron_variant		5
LINC01643	ENST00000652942.1	n.246-23843C>T		intron_variant
LINC01643	ENST00000653369.1	n.115-33960C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128314 AN: 152030 Hom.: 54632 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.844 AC: 128438 AN: 152148 Hom.: 54697 Cov.: 31 AF XY: 0.847 AC XY: 63039 AN XY: 74384

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.833

Alfa AF: 0.820 Hom.: 6396

Bravo AF: 0.848

Asia WGS AF: 0.908 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs141418; hg19: chr22-34533742;