9-21946323-C-T

Variant names:

• chr9-21946323-C-T
• rs2811717
• ENST00000404796.3:n.461-83110C>T

Variant summary

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

The ENST00000404796.3(ENSG00000264545):​n.461-83110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,000 control chromosomes in the GnomAD database, including 43,786 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 (43786 hom., cov: 31)
• Consequence: ENSG00000264545 ENST00000404796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

Genes affected

ENSG00000264545 (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 (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000264545	ENST00000404796.3	n.461-83110C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109100 AN: 151882 Hom.: 43789 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.718 AC: 109121 AN: 152000 Hom.: 43786 Cov.: 31 AF XY: 0.725 AC XY: 53912 AN XY: 74318

African (AFR) AF: 0.322 AC: 13332 AN: 41390

American (AMR) AF: 0.839 AC: 12818 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3082 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5141 AN: 5172

South Asian (SAS) AF: 0.865 AC: 4169 AN: 4820

European-Finnish (FIN) AF: 0.897 AC: 9484 AN: 10572

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58498 AN: 67996

Other (OTH) AF: 0.753 AC: 1584 AN: 2104

Alfa AF: 0.801 Hom.: 16929

Bravo AF: 0.697

Asia WGS AF: 0.860 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		0.10

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2811717; hg19: chr9-21946322;