rs16946931

Variant names:

• chr16-49108595-T-C
• rs16946931
• ENST00000655430.1:n.268+5381A>G

Variant summary

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

The ENST00000655430.1(ENSG00000287469):​n.268+5381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,144 control chromosomes in the GnomAD database, including 3,286 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 0.19 (3286 hom., cov: 32)
• Consequence: ENSG00000287469 ENST00000655430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 4 publications found

Genes affected

ENSG00000287469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655430.1. 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
	ENSG00000287469	ENST00000655430.1		n.268+5381A>G		intron	N/A
	ENSG00000287469	ENST00000659681.1		n.260+5381A>G		intron	N/A
	ENSG00000287469	ENST00000737824.1		n.201+2374A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28924 AN: 152024 Hom.: 3279 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.190 AC: 28930 AN: 152144 Hom.: 3286 Cov.: 32 AF XY: 0.194 AC XY: 14399 AN XY: 74374

African (AFR) AF: 0.0928 AC: 3852 AN: 41528

American (AMR) AF: 0.255 AC: 3892 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2360 AN: 5162

South Asian (SAS) AF: 0.182 AC: 877 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2309 AN: 10598

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13779 AN: 67978

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.180 Hom.: 354

Bravo AF: 0.199

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.42
PhyloP100		1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16946931;

hg19: chr16-49142506;