chr9-26379842-G-A

Variant names:

• chr9-26379842-G-A
• rs439314
• ENST00000844068.1:n.628-33554C>T

Variant summary

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

The ENST00000844068.1(ENSG00000309811):​n.628-33554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,076 control chromosomes in the GnomAD database, including 6,732 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 0.19 (6732 hom., cov: 33)
• Consequence: ENSG00000309811 ENST00000844068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 2 publications found

Genes affected

ENSG00000309811 (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 = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309811	ENST00000844068.1		n.628-33554C>T		intron	N/A
	ENSG00000309811	ENST00000844069.1		n.214-42735C>T		intron	N/A
	ENSG00000309811	ENST00000844070.1		n.205-33554C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28067 AN: 151958 Hom.: 6714 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.185 AC: 28135 AN: 152076 Hom.: 6732 Cov.: 33 AF XY: 0.180 AC XY: 13353 AN XY: 74362

African (AFR) AF: 0.552 AC: 22895 AN: 41442

American (AMR) AF: 0.0870 AC: 1330 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.185 AC: 955 AN: 5158

South Asian (SAS) AF: 0.0881 AC: 425 AN: 4824

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1880 AN: 67982

Other (OTH) AF: 0.141 AC: 298 AN: 2106

Alfa AF: 0.121 Hom.: 1536

Bravo AF: 0.206

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.46
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs439314; hg19: chr9-26379840;