rs764464

Variant names:

• chr2-40823983-A-C
• rs764464
• ENST00000753888.1:n.306+13189T>G

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.306+13189T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,870 control chromosomes in the GnomAD database, including 22,326 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 0.52 (22326 hom., cov: 31)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.44
• Publications: 3 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753888.1. 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
	ENSG00000298207	ENST00000753888.1		n.306+13189T>G		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.306+13189T>G		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.402+13189T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78550 AN: 151752 Hom.: 22326 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.517 AC: 78584 AN: 151870 Hom.: 22326 Cov.: 31 AF XY: 0.520 AC XY: 38607 AN XY: 74224

African (AFR) AF: 0.294 AC: 12186 AN: 41406

American (AMR) AF: 0.453 AC: 6898 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2201 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1827 AN: 5136

South Asian (SAS) AF: 0.716 AC: 3444 AN: 4812

European-Finnish (FIN) AF: 0.645 AC: 6812 AN: 10556

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43287 AN: 67942

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.589 Hom.: 76296

Bravo AF: 0.488

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0070
DANN	Benign	0.47
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs764464; hg19: chr2-41051123;