rs184891496

Variant names:

• chr9-38750582-T-C
• rs184891496
• ENST00000835853.1:n.186-17694T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000835853.1(ENSG00000308694):​n.186-17694T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.017 (38 hom., cov: 19)
• Consequence: ENSG00000308694 ENST00000835853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 0 publications found

Genes affected

ENSG00000308694 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 38 gene

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
ENSG00000308694	ENST00000835853.1	n.186-17694T>C		intron_variant	Intron 1 of 1
ENSG00000308694	ENST00000835854.1	n.376+12374T>C		intron_variant	Intron 3 of 4
ENSG00000308694	ENST00000835855.1	n.73-17694T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0174 AC: 1987 AN: 113976 Hom.: 39 Cov.: 19

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.00256

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00959

Gnomad EAS AF: 0.00146

Gnomad SAS AF: 0.00525

Gnomad FIN AF: 0.00861

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.00680

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

GnomAD4 genome AF: 0.0174 AC: 1988 AN: 113970 Hom.: 38 Cov.: 19 AF XY: 0.0171 AC XY: 943 AN XY: 55180

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0416 AC: 1201 AN: 28862

American (AMR) AF: 0.00779 AC: 98 AN: 12588

Ashkenazi Jewish (ASJ) AF: 0.00959 AC: 27 AN: 2816

East Asian (EAS) AF: 0.00147 AC: 6 AN: 4086

South Asian (SAS) AF: 0.00527 AC: 21 AN: 3982

European-Finnish (FIN) AF: 0.00861 AC: 50 AN: 5806

Middle Eastern (MID) AF: 0.00467 AC: 1 AN: 214

European-Non Finnish (NFE) AF: 0.0107 AC: 570 AN: 53208

Other (OTH) AF: 0.00737 AC: 12 AN: 1628

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.126 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.27
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs184891496; hg19: chr9-38750579;