ENST00000764465.1:n.297+25070G>A

Variant names:

• chr21-22941172-C-T
• rs2827775
• ENST00000764465.1:n.297+25070G>A

Variant summary

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

The ENST00000764465.1(ENSG00000299538):​n.297+25070G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,594 control chromosomes in the GnomAD database, including 19,206 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 (19206 hom., cov: 31)
• Consequence: ENSG00000299538 ENST00000764465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

Genes affected

ENSG00000299538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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
ENSG00000299538	ENST00000764465.1	n.297+25070G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76214 AN: 151476 Hom.: 19183 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.503 AC: 76284 AN: 151594 Hom.: 19206 Cov.: 31 AF XY: 0.505 AC XY: 37369 AN XY: 74066

African (AFR) AF: 0.539 AC: 22308 AN: 41382

American (AMR) AF: 0.510 AC: 7750 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3464

East Asian (EAS) AF: 0.400 AC: 2046 AN: 5114

South Asian (SAS) AF: 0.588 AC: 2826 AN: 4810

European-Finnish (FIN) AF: 0.499 AC: 5245 AN: 10510

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32796 AN: 67834

Other (OTH) AF: 0.496 AC: 1039 AN: 2096

Alfa AF: 0.492 Hom.: 24259

Bravo AF: 0.505

Asia WGS AF: 0.505 AC: 1753 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2827775; hg19: chr21-24313493;