9-90801254-A-G

Variant names:

• chr9-90801254-A-G
• rs290986
• ENST00000831879.1:n.55+3091T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000831879.1(ENSG00000308134):​n.55+3091T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,170 control chromosomes in the GnomAD database, including 3,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3019 hom., cov: 33)
• Consequence: ENSG00000308134 ENST00000831879.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200
• Publications: 28 publications found

Genes affected

ENSG00000308134 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 9-90801254-A-G is Benign according to our data. Variant chr9-90801254-A-G is described in ClinVar as Benign. ClinVar VariationId is 1275221.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831879.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308134	ENST00000831879.1		n.55+3091T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28775 AN: 152052 Hom.: 3023 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.189 AC: 28777 AN: 152170 Hom.: 3019 Cov.: 33 AF XY: 0.192 AC XY: 14299 AN XY: 74376

African (AFR) AF: 0.129 AC: 5341 AN: 41550

American (AMR) AF: 0.203 AC: 3103 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2259 AN: 5150

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4824

European-Finnish (FIN) AF: 0.258 AC: 2731 AN: 10566

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12997 AN: 67988

Other (OTH) AF: 0.194 AC: 410 AN: 2116

Alfa AF: 0.194 Hom.: 12961

Bravo AF: 0.185

Asia WGS AF: 0.309 AC: 1079 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs290986; hg19: chr9-93563536;