rs448261

Variant names:

• chr4-176516966-G-A
• rs448261
• ENST00000752489.1:n.172-3338G>A

Variant summary

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

The ENST00000752489.1(ENSG00000298014):​n.172-3338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,056 control chromosomes in the GnomAD database, including 26,140 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 0.59 (26140 hom., cov: 29)
• Consequence: ENSG00000298014 ENST00000752489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 3 publications found

Genes affected

ENSG00000298014 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752489.1. 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
	ENSG00000298014	ENST00000752489.1		n.172-3338G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88448 AN: 150938 Hom.: 26106 Cov.: 29

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.586 AC: 88534 AN: 151056 Hom.: 26140 Cov.: 29 AF XY: 0.585 AC XY: 43163 AN XY: 73744

African (AFR) AF: 0.653 AC: 26840 AN: 41104

American (AMR) AF: 0.578 AC: 8782 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3468

East Asian (EAS) AF: 0.407 AC: 2086 AN: 5124

South Asian (SAS) AF: 0.591 AC: 2828 AN: 4788

European-Finnish (FIN) AF: 0.569 AC: 5852 AN: 10278

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38497 AN: 67784

Other (OTH) AF: 0.596 AC: 1253 AN: 2102

Alfa AF: 0.603 Hom.: 4815

Bravo AF: 0.584

Asia WGS AF: 0.507 AC: 1759 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.44
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs448261; hg19: chr4-177438117;