ENST00000425894.2:n.461+14165A>C

Variant names:

• chr3-5757998-A-C
• rs721213
• ENST00000425894.2:n.461+14165A>C

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.461+14165A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,088 control chromosomes in the GnomAD database, including 10,782 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 0.36 (10782 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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+14165A>C		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.212+61512A>C		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.232+61512A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54868 AN: 151970 Hom.: 10779 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.361 AC: 54876 AN: 152088 Hom.: 10782 Cov.: 32 AF XY: 0.365 AC XY: 27154 AN XY: 74336

African (AFR) AF: 0.215 AC: 8941 AN: 41512

American (AMR) AF: 0.428 AC: 6536 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3584 AN: 5154

South Asian (SAS) AF: 0.484 AC: 2328 AN: 4808

European-Finnish (FIN) AF: 0.432 AC: 4565 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26565 AN: 67970

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.376 Hom.: 25085

Bravo AF: 0.353

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs721213; hg19: chr3-5799685;