8-123678720-T-G

Variant names:

• chr8-123678720-T-G
• rs4242345
• ENST00000836608.1:n.119-33972T>G

Variant summary

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

The ENST00000836608.1(ENSG00000253286):​n.119-33972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,084 control chromosomes in the GnomAD database, including 21,364 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 0.53 (21364 hom., cov: 32)
• Consequence: ENSG00000253286 ENST00000836608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 4 publications found

Genes affected

ENSG00000253286 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 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
ENSG00000253286	ENST00000836608.1	n.119-33972T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80216 AN: 151966 Hom.: 21352 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.528 AC: 80272 AN: 152084 Hom.: 21364 Cov.: 32 AF XY: 0.528 AC XY: 39229 AN XY: 74366

African (AFR) AF: 0.534 AC: 22125 AN: 41466

American (AMR) AF: 0.461 AC: 7042 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1955 AN: 5170

South Asian (SAS) AF: 0.608 AC: 2929 AN: 4820

European-Finnish (FIN) AF: 0.559 AC: 5922 AN: 10590

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36758 AN: 67964

Other (OTH) AF: 0.512 AC: 1079 AN: 2108

Alfa AF: 0.529 Hom.: 64672

Bravo AF: 0.514

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.83
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4242345; hg19: chr8-124690960;