8-100476593-A-C

Variant names:

• chr8-100476593-A-C
• rs2844043
• ENST00000667762.2:n.927A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667762.2(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 ENST00000667762.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 3 publications found

Genes affected

ENSG00000253666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667762.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253666	ENST00000667762.2		n.927A>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000253666	ENST00000521851.1	TSL:4	n.162+757A>C		intron	N/A
	ENSG00000253666	ENST00000523784.2	TSL:3	n.505-15894A>C		intron	N/A

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

African (AFR) AF: 0.183 AC: 7601 AN: 41450

American (AMR) AF: 0.386 AC: 5896 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1666 AN: 5180

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4812

European-Finnish (FIN) AF: 0.534 AC: 5581 AN: 10448

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33538 AN: 67944

Other (OTH) AF: 0.376 AC: 791 AN: 2106

Alfa AF: 0.445 Hom.: 31380

Bravo AF: 0.367

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.83
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2844043; hg19: chr8-101488821;