rs2844043

Positions:

• chr8-100476593-A-C
• chr8-100476593-A-T

Variant summary

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

The ENST00000667762.1(ENSG00000253666):​n.927A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,876 control chromosomes in the GnomAD database, including 12,755 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 0.38 (12755 hom., cov: 31)
• Consequence: ENSG00000253666 ENST00000667762.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

Genes affected

ENSG00000253666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100476593A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253666	ENST00000667762.1	n.927A>C		non_coding_transcript_exon_variant	1/1
ENSG00000253666	ENST00000521851.1	n.162+757A>C		intron_variant		4
ENSG00000253666	ENST00000523831.1	n.147+757A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58188 AN: 151758 Hom.: 12754 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.383 AC: 58194 AN: 151876 Hom.: 12755 Cov.: 31 AF XY: 0.382 AC XY: 28318 AN XY: 74200

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.376

Alfa AF: 0.454 Hom.: 9687

Bravo AF: 0.367

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844043; hg19: chr8-101488821;