5-159403811-G-A

Variant names:

• chr5-159403811-G-A
• rs4921226
• ENST00000635333.1:n.327+11234G>A

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.327+11234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,024 control chromosomes in the GnomAD database, including 8,010 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 0.30 (8010 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 9 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635333.1. 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
	ENSG00000249738	ENST00000635333.1	TSL:5	n.327+11234G>A		intron	N/A
	ENSG00000249738	ENST00000641150.1		n.533-12713G>A		intron	N/A
	ENSG00000249738	ENST00000648969.1		n.54-12713G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45460 AN: 151906 Hom.: 8009 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.299 AC: 45467 AN: 152024 Hom.: 8010 Cov.: 31 AF XY: 0.309 AC XY: 22970 AN XY: 74300

African (AFR) AF: 0.114 AC: 4733 AN: 41476

American (AMR) AF: 0.369 AC: 5645 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1313 AN: 5158

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4814

European-Finnish (FIN) AF: 0.471 AC: 4966 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24172 AN: 67968

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.336 Hom.: 11290

Bravo AF: 0.280

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4921226; hg19: chr5-158830819;