chr8-125391906-C-T

Variant names:

• chr8-125391906-C-T
• rs4332153
• ENST00000839543.1:n.149-1623C>T

Variant summary

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

The ENST00000839543.1(ENSG00000309211):​n.149-1623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,104 control chromosomes in the GnomAD database, including 9,956 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 0.33 (9956 hom., cov: 31)
• Consequence: ENSG00000309211 ENST00000839543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 0 publications found

Genes affected

ENSG00000309211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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
ENSG00000309211	ENST00000839543.1	n.149-1623C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49977 AN: 151984 Hom.: 9950 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.329 AC: 49982 AN: 152104 Hom.: 9956 Cov.: 31 AF XY: 0.327 AC XY: 24321 AN XY: 74370

African (AFR) AF: 0.126 AC: 5210 AN: 41514

American (AMR) AF: 0.314 AC: 4796 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3470

East Asian (EAS) AF: 0.126 AC: 654 AN: 5178

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4822

European-Finnish (FIN) AF: 0.420 AC: 4436 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30386 AN: 67964

Other (OTH) AF: 0.315 AC: 664 AN: 2106

Alfa AF: 0.399 Hom.: 42779

Bravo AF: 0.308

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.65
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4332153; hg19: chr8-126404148;