9-21946323-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000264545 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.753

Alfa AF: 0.797 Hom.: 8421

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2811717; hg19: chr9-21946322;