ENST00000563124.2:n.535A>G

Variant names:

• chr16-49922283-T-C
• rs4785367
• ENST00000563124.2:n.535A>G

Variant summary

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

The ENST00000563124.2(ENSG00000261751):​n.535A>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: ENSG00000261751 ENST00000563124.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 7 publications found

Genes affected

ENSG00000261751 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261751	ENST00000563124.2	n.535A>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000261751	ENST00000793345.1	n.261A>G		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 9 AN: 24

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.643 AC: 26680 AN: 41480

American (AMR) AF: 0.440 AC: 6729 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1793 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5164

South Asian (SAS) AF: 0.611 AC: 2951 AN: 4830

European-Finnish (FIN) AF: 0.455 AC: 4804 AN: 10566

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33787 AN: 67964

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.505 Hom.: 86774

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4785367; hg19: chr16-49956194;