chr16-48522662-G-T

Variant names:

• chr16-48522662-G-T
• rs9933187
• ENST00000730337.1:n.432-15716G>T

Variant summary

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

The ENST00000730337.1(ENSG00000295475):​n.432-15716G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,038 control chromosomes in the GnomAD database, including 11,623 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 0.38 (11623 hom., cov: 32)
• Consequence: ENSG00000295475 ENST00000730337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 8 publications found

Genes affected

ENSG00000295475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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
ENSG00000295475	ENST00000730337.1	n.432-15716G>T		intron_variant	Intron 2 of 2
ENSG00000295475	ENST00000730338.1	n.230+9698G>T		intron_variant	Intron 1 of 2
ENSG00000295475	ENST00000730339.1	n.230+9698G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57441 AN: 151920 Hom.: 11611 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.378 AC: 57488 AN: 152038 Hom.: 11623 Cov.: 32 AF XY: 0.378 AC XY: 28094 AN XY: 74306

African (AFR) AF: 0.518 AC: 21453 AN: 41440

American (AMR) AF: 0.393 AC: 6013 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3468

East Asian (EAS) AF: 0.193 AC: 999 AN: 5174

South Asian (SAS) AF: 0.291 AC: 1406 AN: 4830

European-Finnish (FIN) AF: 0.377 AC: 3989 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21440 AN: 67954

Other (OTH) AF: 0.365 AC: 772 AN: 2114

Alfa AF: 0.337 Hom.: 33629

Bravo AF: 0.389

Asia WGS AF: 0.271 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.83
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs9933187; hg19: chr16-48556573;