9-85381389-A-G

Variant names:

• chr9-85381389-A-G
• rs2841443
• ENST00000648131.1:n.601-8429T>C

Variant summary

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

The ENST00000648131.1(ENSG00000285634):​n.601-8429T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,276 control chromosomes in the GnomAD database, including 60,222 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 0.89 (60222 hom., cov: 32)
• Consequence: ENSG00000285634 ENST00000648131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 2 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 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
ENSG00000285634	ENST00000648131.1	n.601-8429T>C		intron_variant	Intron 3 of 3
ENSG00000285634	ENST00000662737.1	n.1681-8429T>C		intron_variant	Intron 2 of 2
ENSG00000285634	ENST00000669133.1	n.283-8429T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134907 AN: 152158 Hom.: 60159 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.887 AC: 135028 AN: 152276 Hom.: 60222 Cov.: 32 AF XY: 0.886 AC XY: 65957 AN XY: 74448

African (AFR) AF: 0.972 AC: 40397 AN: 41582

American (AMR) AF: 0.768 AC: 11743 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2993 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4812 AN: 5180

South Asian (SAS) AF: 0.896 AC: 4316 AN: 4816

European-Finnish (FIN) AF: 0.897 AC: 9512 AN: 10602

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58510 AN: 68016

Other (OTH) AF: 0.878 AC: 1857 AN: 2114

Alfa AF: 0.861 Hom.: 74464

Bravo AF: 0.878

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.67
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2841443; hg19: chr9-87996304;