8-20374603-T-C

Variant names:

• chr8-20374603-T-C
• rs34393111
• ENST00000822544.1:n.301+14823T>C

Variant summary

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

The ENST00000822544.1(ENSG00000253164):​n.301+14823T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,962 control chromosomes in the GnomAD database, including 10,653 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 0.35 (10653 hom., cov: 31)
• Consequence: ENSG00000253164 ENST00000822544.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 1 publications found

Genes affected

ENSG00000253164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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
ENSG00000253164	ENST00000822544.1	n.301+14823T>C		intron_variant	Intron 2 of 2
ENSG00000253164	ENST00000822545.1	n.445+14823T>C		intron_variant	Intron 3 of 3
ENSG00000253164	ENST00000822546.1	n.422+1878T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53219 AN: 151842 Hom.: 10644 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53263 AN: 151962 Hom.: 10653 Cov.: 31 AF XY: 0.360 AC XY: 26757 AN XY: 74268

African (AFR) AF: 0.167 AC: 6909 AN: 41486

American (AMR) AF: 0.393 AC: 5999 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3364 AN: 5142

South Asian (SAS) AF: 0.589 AC: 2828 AN: 4804

European-Finnish (FIN) AF: 0.443 AC: 4679 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26787 AN: 67918

Other (OTH) AF: 0.351 AC: 740 AN: 2106

Alfa AF: 0.351 Hom.: 1268

Bravo AF: 0.335

Asia WGS AF: 0.578 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs34393111; hg19: chr8-20232114;