rs4921496

Variant names:

• chr5-159421063-T-C
• rs4921496
• ENST00000635333.1:n.446-2960T>C

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.446-2960T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,176 control chromosomes in the GnomAD database, including 46,801 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 0.78 (46801 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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.446-2960T>C		intron	N/A
	ENSG00000249738	ENST00000648969.1		n.172-2960T>C		intron	N/A
	ENSG00000249738	ENST00000764988.1		n.803-2960T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119098 AN: 152058 Hom.: 46763 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.783 AC: 119188 AN: 152176 Hom.: 46801 Cov.: 32 AF XY: 0.790 AC XY: 58749 AN XY: 74410

African (AFR) AF: 0.777 AC: 32232 AN: 41482

American (AMR) AF: 0.847 AC: 12955 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2915 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4478 AN: 5186

South Asian (SAS) AF: 0.803 AC: 3874 AN: 4824

European-Finnish (FIN) AF: 0.819 AC: 8694 AN: 10612

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51348 AN: 67984

Other (OTH) AF: 0.814 AC: 1723 AN: 2116

Alfa AF: 0.768 Hom.: 131642

Bravo AF: 0.786

Asia WGS AF: 0.850 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.80
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4921496; hg19: chr5-158848071;