rs4921496

Positions:

• chr5-159421063-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635333.1(ENSG00000249738):​n.446-2960T>C variant causes a intron, non coding transcript 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: ENST00000635333.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635333.1	n.446-2960T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000648969.1	n.172-2960T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.814

Alfa AF: 0.767 Hom.: 88772

Bravo AF: 0.786

Asia WGS AF: 0.850 AC: 2953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4921496; hg19: chr5-158848071;