chr8-80378152-C-T

Variant names:

• chr8-80378152-C-T
• rs2370615
• ENST00000644465.1:n.254-70545C>T

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.254-70545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,746 control chromosomes in the GnomAD database, including 21,187 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 0.51 (21187 hom., cov: 29)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 12 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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.254-70545C>T		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656157.2	n.285+89150C>T		intron_variant	Intron 2 of 3
ENSG00000253238	ENST00000656811.1	n.252-24584C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76646 AN: 151628 Hom.: 21193 Cov.: 29

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.505 AC: 76641 AN: 151746 Hom.: 21187 Cov.: 29 AF XY: 0.508 AC XY: 37660 AN XY: 74162

African (AFR) AF: 0.273 AC: 11305 AN: 41350

American (AMR) AF: 0.538 AC: 8201 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2238 AN: 5152

South Asian (SAS) AF: 0.526 AC: 2524 AN: 4794

European-Finnish (FIN) AF: 0.664 AC: 6988 AN: 10526

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41651 AN: 67910

Other (OTH) AF: 0.525 AC: 1106 AN: 2108

Alfa AF: 0.436 Hom.: 1532

Bravo AF: 0.480

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.7
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2370615; hg19: chr8-81290387;