16-35877214-G-A

Variant names:

• chr16-35877214-G-A
• rs12933929
• ENST00000802595.1:n.246+3813G>A

Variant summary

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

The ENST00000802595.1(ENSG00000304337):​n.246+3813G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,984 control chromosomes in the GnomAD database, including 10,221 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 0.33 (10221 hom., cov: 32)
• Consequence: ENSG00000304337 ENST00000802595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 8 publications found

Genes affected

ENSG00000304337 (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 (NFE) allele frequency at 95% confidence interval = 0.452 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
ENSG00000304337	ENST00000802595.1	n.246+3813G>A		intron_variant	Intron 2 of 2
ENSG00000304337	ENST00000802596.1	n.271+3813G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49929 AN: 151866 Hom.: 10218 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.329 AC: 49942 AN: 151984 Hom.: 10221 Cov.: 32 AF XY: 0.322 AC XY: 23924 AN XY: 74288

African (AFR) AF: 0.101 AC: 4199 AN: 41494

American (AMR) AF: 0.424 AC: 6480 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3462

East Asian (EAS) AF: 0.0951 AC: 490 AN: 5154

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3834 AN: 10532

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30972 AN: 67924

Other (OTH) AF: 0.354 AC: 747 AN: 2110

Alfa AF: 0.323 Hom.: 3197

Bravo AF: 0.327

Asia WGS AF: 0.146 AC: 510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs12933929; hg19: chr16-35111585;