ENST00000425894.2:n.461+16366G>A

Variant names:

• chr3-5760199-G-A
• rs1836577
• ENST00000425894.2:n.461+16366G>A

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.461+16366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,756 control chromosomes in the GnomAD database, including 19,941 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 0.51 (19941 hom., cov: 30)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.461+16366G>A		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.212+63713G>A		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.232+63713G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77089 AN: 151638 Hom.: 19930 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.508 AC: 77135 AN: 151756 Hom.: 19941 Cov.: 30 AF XY: 0.513 AC XY: 38044 AN XY: 74126

African (AFR) AF: 0.410 AC: 16943 AN: 41330

American (AMR) AF: 0.500 AC: 7629 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2448 AN: 5140

South Asian (SAS) AF: 0.586 AC: 2816 AN: 4806

European-Finnish (FIN) AF: 0.620 AC: 6510 AN: 10506

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37317 AN: 67946

Other (OTH) AF: 0.490 AC: 1034 AN: 2110

Alfa AF: 0.532 Hom.: 35326

Bravo AF: 0.494

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.067
DANN	Benign	0.85
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1836577; hg19: chr3-5801886;