rs1374633

Positions:

• chr8-93290514-C-T

Variant summary

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

The ENST00000522598.1(ENSG00000254089):​n.40-3140C>T 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 0.183 in 152,216 control chromosomes in the GnomAD database, including 2,855 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 (2855 hom., cov: 33)
• Consequence: ENST00000522598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

(HGNC:):

CIBAR1-DT (HGNC:43644): (CIBAR1 divergent transcript)

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 (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986956	XR_001745996.1	n.193+12411G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522598.1	n.40-3140C>T		intron_variant, non_coding_transcript_variant		3
CIBAR1-DT	ENST00000520096.5	n.579+12411G>A		intron_variant, non_coding_transcript_variant		3
CIBAR1-DT	ENST00000520513.1	n.86+2087G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27779 AN: 152098 Hom.: 2856 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 27790 AN: 152216 Hom.: 2855 Cov.: 33 AF XY: 0.182 AC XY: 13529 AN XY: 74414

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0888

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.185

Alfa AF: 0.218 Hom.: 1656

Bravo AF: 0.174

Asia WGS AF: 0.142 AC: 495 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	0.023
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374633; hg19: chr8-94302742;