8-80445467-C-T

Variant names:

• chr8-80445467-C-T
• rs400824
• ENST00000644465.1:n.254-3230C>T

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.254-3230C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,072 control chromosomes in the GnomAD database, including 19,739 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 0.45 (19739 hom., cov: 32)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 9 publications found

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644465.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253238	ENST00000644465.1		n.254-3230C>T		intron	N/A
	ENSG00000253238	ENST00000656157.2		n.286-37141C>T		intron	N/A
	ENSG00000253238	ENST00000662273.2		n.371-37141C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67967 AN: 151954 Hom.: 19688 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.448 AC: 68067 AN: 152072 Hom.: 19739 Cov.: 32 AF XY: 0.439 AC XY: 32666 AN XY: 74356

African (AFR) AF: 0.830 AC: 34433 AN: 41486

American (AMR) AF: 0.334 AC: 5099 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3472

East Asian (EAS) AF: 0.175 AC: 906 AN: 5182

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4822

European-Finnish (FIN) AF: 0.234 AC: 2476 AN: 10578

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21004 AN: 67954

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.343 Hom.: 5240

Bravo AF: 0.470

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs400824; hg19: chr8-81357702;