1-33465515-G-A

Variant names:

• chr1-33465515-G-A
• rs4653152
• ENST00000801136.1:n.408-188C>T

Variant summary

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

The ENST00000801136.1(ENSG00000304221):​n.408-188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,902 control chromosomes in the GnomAD database, including 5,226 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 0.26 (5226 hom., cov: 31)
• Consequence: ENSG00000304221 ENST00000801136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 0 publications found

Genes affected

ENSG00000304221 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801136.1. 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
	ENSG00000304221	ENST00000801136.1		n.408-188C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39187 AN: 151784 Hom.: 5221 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.258 AC: 39208 AN: 151902 Hom.: 5226 Cov.: 31 AF XY: 0.259 AC XY: 19256 AN XY: 74246

African (AFR) AF: 0.206 AC: 8535 AN: 41438

American (AMR) AF: 0.235 AC: 3587 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5168

South Asian (SAS) AF: 0.362 AC: 1743 AN: 4812

European-Finnish (FIN) AF: 0.265 AC: 2789 AN: 10540

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18984 AN: 67906

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.254 Hom.: 3287

Bravo AF: 0.250

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.22
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4653152; hg19: chr1-33931116; COSMIC: COSV69405510;