16-13728502-C-T

Variant names:

• chr16-13728502-C-T
• rs179619
• ENST00000740799.1:n.244-9700G>A

Variant summary

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

The ENST00000740799.1(ENSG00000262267):​n.244-9700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,098 control chromosomes in the GnomAD database, including 44,585 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 0.76 (44585 hom., cov: 32)
• Consequence: ENSG00000262267 ENST00000740799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 6 publications found

Genes affected

ENSG00000262267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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
ENSG00000262267	ENST00000740799.1	n.244-9700G>A		intron_variant	Intron 1 of 2
ENSG00000262267	ENST00000740800.1	n.409-9700G>A		intron_variant	Intron 3 of 3
ENSG00000262267	ENST00000740801.1	n.249-9700G>A		intron_variant	Intron 1 of 1
ENSG00000262267	ENST00000659657.1	n.*152G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115989 AN: 151980 Hom.: 44560 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.763 AC: 116068 AN: 152098 Hom.: 44585 Cov.: 32 AF XY: 0.766 AC XY: 56948 AN XY: 74348

African (AFR) AF: 0.716 AC: 29703 AN: 41494

American (AMR) AF: 0.690 AC: 10545 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4580 AN: 5166

South Asian (SAS) AF: 0.767 AC: 3698 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8989 AN: 10586

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53644 AN: 67976

Other (OTH) AF: 0.735 AC: 1544 AN: 2102

Alfa AF: 0.776 Hom.: 127361

Bravo AF: 0.748

Asia WGS AF: 0.764 AC: 2651 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs179619; hg19: chr16-13822359;