rs9332421

Variant names:

• chr2-76643613-A-G
• rs9332421
• ENST00000665445.1:n.2334-10078T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-76643613-A-G
• chr2-76643613-A-T

Variant summary

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

The ENST00000665445.1(ENSG00000287026):​n.2334-10078T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,930 control chromosomes in the GnomAD database, including 19,664 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 0.50 (19664 hom., cov: 31)
• Consequence: ENSG00000287026 ENST00000665445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 3 publications found

Genes affected

ENSG00000287026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665445.1. 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
	ENSG00000287026	ENST00000665445.1		n.2334-10078T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76475 AN: 151810 Hom.: 19655 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.504 AC: 76507 AN: 151930 Hom.: 19664 Cov.: 31 AF XY: 0.505 AC XY: 37499 AN XY: 74254

African (AFR) AF: 0.418 AC: 17332 AN: 41446

American (AMR) AF: 0.463 AC: 7059 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2179 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1956 AN: 5150

South Asian (SAS) AF: 0.523 AC: 2517 AN: 4814

European-Finnish (FIN) AF: 0.602 AC: 6356 AN: 10554

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37400 AN: 67930

Other (OTH) AF: 0.492 AC: 1039 AN: 2110

Alfa AF: 0.530 Hom.: 67567

Bravo AF: 0.486

Asia WGS AF: 0.453 AC: 1577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		0.063

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9332421;

hg19: chr2-76870739;