rs353873

Variant names:

• chr4-166200821-C-T
• rs353873
• ENST00000835335.1:n.294+1808C>T

Variant summary

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

The ENST00000835335.1(ENSG00000308604):​n.294+1808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,056 control chromosomes in the GnomAD database, including 40,703 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 0.72 (40703 hom., cov: 32)
• Consequence: ENSG00000308604 ENST00000835335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 0 publications found

Genes affected

ENSG00000308604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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
ENSG00000308604	ENST00000835335.1	n.294+1808C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109221 AN: 151938 Hom.: 40695 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.719 AC: 109272 AN: 152056 Hom.: 40703 Cov.: 32 AF XY: 0.721 AC XY: 53628 AN XY: 74352

African (AFR) AF: 0.536 AC: 22219 AN: 41428

American (AMR) AF: 0.742 AC: 11332 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2315 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2323 AN: 5156

South Asian (SAS) AF: 0.832 AC: 4017 AN: 4826

European-Finnish (FIN) AF: 0.869 AC: 9199 AN: 10582

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55338 AN: 68000

Other (OTH) AF: 0.711 AC: 1504 AN: 2114

Alfa AF: 0.769 Hom.: 5698

Bravo AF: 0.695

Asia WGS AF: 0.661 AC: 2299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.56
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs353873; hg19: chr4-167121973;