ENST00000644465.1:n.253+66918T>C

Variant names:

• chr8-80355920-T-C
• rs6473223
• ENST00000644465.1:n.253+66918T>C

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.253+66918T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,980 control chromosomes in the GnomAD database, including 28,886 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 0.61 (28886 hom., cov: 31)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 20 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 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
ENSG00000253238	ENST00000644465.1	n.253+66918T>C		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656157.2	n.285+66918T>C		intron_variant	Intron 2 of 3
ENSG00000253238	ENST00000656811.1	n.252-46816T>C		intron_variant	Intron 2 of 2
ENSG00000253238	ENST00000662273.2	n.370+66918T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93089 AN: 151862 Hom.: 28872 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.613 AC: 93145 AN: 151980 Hom.: 28886 Cov.: 31 AF XY: 0.611 AC XY: 45407 AN XY: 74264

African (AFR) AF: 0.587 AC: 24329 AN: 41446

American (AMR) AF: 0.562 AC: 8583 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2062 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2044 AN: 5154

South Asian (SAS) AF: 0.546 AC: 2625 AN: 4808

European-Finnish (FIN) AF: 0.688 AC: 7265 AN: 10554

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43984 AN: 67976

Other (OTH) AF: 0.620 AC: 1305 AN: 2106

Alfa AF: 0.620 Hom.: 22568

Bravo AF: 0.597

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs6473223; hg19: chr8-81268155;