chr16-23754453-G-A

Variant names:

• chr16-23754453-G-A
• rs4968031
• ENST00000623305.1:n.1487C>T

Variant summary

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

The ENST00000623305.1(ENSG00000279756):​n.1487C>T 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 0.0751 in 152,428 control chromosomes in the GnomAD database, including 740 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 0.075 (740 hom., cov: 32)
  • Exomes 𝑓: 0.049 (0 hom.)
• Consequence: ENSG00000279756 ENST00000623305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 8 publications found

Genes affected

ENSG00000279756 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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
ENSG00000279756	ENST00000623305.1	n.1487C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11414 AN: 152086 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0818

GnomAD4 exome AF: 0.0491 AC: 11 AN: 224 Hom.: 0 Cov.: 0 AF XY: 0.0574 AC XY: 7 AN XY: 122

African (AFR) AF: 0.200 AC: 2 AN: 10

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.167 AC: 1 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0407 AC: 7 AN: 172

Other (OTH) AF: 0.0625 AC: 1 AN: 16

GnomAD4 genome AF: 0.0751 AC: 11430 AN: 152204 Hom.: 740 Cov.: 32 AF XY: 0.0726 AC XY: 5401 AN XY: 74434

African (AFR) AF: 0.175 AC: 7258 AN: 41488

American (AMR) AF: 0.0567 AC: 867 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0584 AC: 282 AN: 4826

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0382 AC: 2595 AN: 68010

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0497 Hom.: 912

Bravo AF: 0.0832

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		-0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.98

Splicing

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

Other links and lift over

dbSNP: rs4968031; hg19: chr16-23765774;