ENST00000816098.1:n.291+18035C>T

Variant names:

• chr9-2212546-G-A
• rs1535842
• ENST00000816098.1:n.291+18035C>T

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.291+18035C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,020 control chromosomes in the GnomAD database, including 26,970 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 0.58 (26970 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 publications found

Genes affected

ENSG00000306181 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816098.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306181	ENST00000816098.1		n.291+18035C>T		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.295+18035C>T		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.272+18035C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87826 AN: 151902 Hom.: 26947 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87890 AN: 152020 Hom.: 26970 Cov.: 32 AF XY: 0.572 AC XY: 42519 AN XY: 74302

African (AFR) AF: 0.793 AC: 32901 AN: 41498

American (AMR) AF: 0.497 AC: 7593 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3464

East Asian (EAS) AF: 0.466 AC: 2406 AN: 5166

South Asian (SAS) AF: 0.516 AC: 2483 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4745 AN: 10546

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34162 AN: 67930

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.535 Hom.: 38804

Bravo AF: 0.593

Asia WGS AF: 0.488 AC: 1700 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.59
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1535842; hg19: chr9-2212546;