chr8-92571795-A-T

Variant names:

• chr8-92571795-A-T
• rs2618134
• ENST00000523284.3:n.480-2729T>A

Variant summary

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

The ENST00000523284.3(ENSG00000253634):​n.480-2729T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,846 control chromosomes in the GnomAD database, including 4,748 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 0.20 (4748 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000523284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 1 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523284.3. 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
	LOC102724710	NR_125827.1		n.396-2729T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253634	ENST00000523284.3	TSL:3	n.480-2729T>A		intron	N/A
	ENSG00000253634	ENST00000648652.1		n.471-2729T>A		intron	N/A
	ENSG00000253634	ENST00000653143.2		n.484-2729T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30950 AN: 151728 Hom.: 4733 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.204 AC: 31014 AN: 151846 Hom.: 4748 Cov.: 32 AF XY: 0.204 AC XY: 15113 AN XY: 74226

African (AFR) AF: 0.422 AC: 17464 AN: 41400

American (AMR) AF: 0.207 AC: 3148 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1389 AN: 5128

South Asian (SAS) AF: 0.126 AC: 606 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10574

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6440 AN: 67928

Other (OTH) AF: 0.182 AC: 384 AN: 2108

Alfa AF: 0.0526 Hom.: 50

Bravo AF: 0.220

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		-0.0090
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2618134; hg19: chr8-93584023;