16-31336427-A-G

Variant names:

• chr16-31336427-A-G
• rs3925075
• ENST00000777754.1:n.571-10719T>C

Variant summary

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

The ENST00000777754.1(ENSG00000289930):​n.571-10719T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,120 control chromosomes in the GnomAD database, including 17,316 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 0.47 (17316 hom., cov: 33)
• Consequence: ENSG00000289930 ENST00000777754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 32 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777754.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289930	ENST00000777754.1		n.571-10719T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71413 AN: 152002 Hom.: 17321 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.469 AC: 71415 AN: 152120 Hom.: 17316 Cov.: 33 AF XY: 0.464 AC XY: 34527 AN XY: 74372

African (AFR) AF: 0.392 AC: 16277 AN: 41488

American (AMR) AF: 0.421 AC: 6441 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3542 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1020 AN: 4830

European-Finnish (FIN) AF: 0.475 AC: 5027 AN: 10580

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35581 AN: 67968

Other (OTH) AF: 0.489 AC: 1032 AN: 2112

Alfa AF: 0.509 Hom.: 92300

Bravo AF: 0.470

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs3925075; hg19: chr16-31347748;