chr16-31336912-A-C

Variant names:

• chr16-31336912-A-C
• rs4075052
• ENST00000777754.1:n.571-11204T>G

Variant summary

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

The ENST00000777754.1(ENSG00000289930):​n.571-11204T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,186 control chromosomes in the GnomAD database, including 41,319 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 0.73 (41319 hom., cov: 32)
• Consequence: ENSG00000289930 ENST00000777754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 21 publications found

Genes affected

ENSG00000289930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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
ENSG00000289930	ENST00000777754.1	n.571-11204T>G		intron_variant	Intron 2 of 2
ENSG00000289930	ENST00000777755.1	n.*39T>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110606 AN: 152068 Hom.: 41284 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.727 AC: 110692 AN: 152186 Hom.: 41319 Cov.: 32 AF XY: 0.719 AC XY: 53493 AN XY: 74398

African (AFR) AF: 0.900 AC: 37386 AN: 41558

American (AMR) AF: 0.605 AC: 9253 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2802 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3613 AN: 5174

South Asian (SAS) AF: 0.464 AC: 2234 AN: 4818

European-Finnish (FIN) AF: 0.607 AC: 6418 AN: 10568

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46612 AN: 68002

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.711 Hom.: 50586

Bravo AF: 0.740

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.31
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4075052; hg19: chr16-31348233;