rs4785367

Positions:

• chr16-49922283-T-C

Variant summary

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

The ENST00000563124.1(ENSG00000261751):​n.532A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,110 control chromosomes in the GnomAD database, including 21,707 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 0.53 (21705 hom., cov: 33)
  • Exomes 𝑓: 0.38 (2 hom.)
• Consequence: ENST00000563124.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000563124.1	n.532A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80054 AN: 151968 Hom.: 21662 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.566

GnomAD4 exome AF: 0.375 AC: 9 AN: 24 Hom.: 2 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.527 AC: 80143 AN: 152086 Hom.: 21705 Cov.: 33 AF XY: 0.522 AC XY: 38826 AN XY: 74338

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.567

Alfa AF: 0.502 Hom.: 40073

Bravo AF: 0.525

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4785367; hg19: chr16-49956194;