16-13704275-C-T

Variant names:

• chr16-13704275-C-T
• rs12927885
• ENST00000740799.1:n.327-581G>A

Variant summary

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

The ENST00000740799.1(ENSG00000262267):​n.327-581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,994 control chromosomes in the GnomAD database, including 9,911 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 0.36 (9911 hom., cov: 33)
• Consequence: ENSG00000262267 ENST00000740799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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.327-581G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54192 AN: 151876 Hom.: 9899 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.357 AC: 54232 AN: 151994 Hom.: 9911 Cov.: 33 AF XY: 0.351 AC XY: 26065 AN XY: 74282

African (AFR) AF: 0.381 AC: 15792 AN: 41458

American (AMR) AF: 0.290 AC: 4439 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3468

East Asian (EAS) AF: 0.141 AC: 732 AN: 5174

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4802

European-Finnish (FIN) AF: 0.379 AC: 3995 AN: 10548

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25213 AN: 67944

Other (OTH) AF: 0.368 AC: 779 AN: 2114

Alfa AF: 0.353 Hom.: 4540

Bravo AF: 0.349

Asia WGS AF: 0.225 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs12927885; hg19: chr16-13798132;