rs4921226

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-159403811-G-A
• chr5-159403811-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000635333.1	n.327+11234G>A		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-12713G>A		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-12713G>A		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.316

Alfa AF: 0.338 Hom.: 9510

Bravo AF: 0.280

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4921226; hg19: chr5-158830819;