rs2844043

Variant names:

• chr8-100476593-A-C
• rs2844043
• ENST00000667762.1:n.927A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-100476593-A-C
• chr8-100476593-A-G
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253666	ENST00000667762.1	n.927A>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000253666	ENST00000521851.1	n.162+757A>C		intron_variant	Intron 1 of 1	4
ENSG00000253666	ENST00000523831.1	n.147+757A>C		intron_variant	Intron 1 of 1	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;