16-13678742-G-T

Variant names:

• chr16-13678742-G-T
• rs2051545
• ENST00000727119.1:n.212+23859C>A

Variant summary

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

The ENST00000727119.1(ENSG00000294970):​n.212+23859C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,886 control chromosomes in the GnomAD database, including 12,745 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 0.40 (12745 hom., cov: 31)
• Consequence: ENSG00000294970 ENST00000727119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 2 publications found

Genes affected

ENSG00000294970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727119.1. 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
	ENSG00000294970	ENST00000727119.1		n.212+23859C>A		intron	N/A
	ENSG00000294970	ENST00000727120.1		n.175-4909C>A		intron	N/A
	ENSG00000294970	ENST00000727121.1		n.84-13094C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60890 AN: 151768 Hom.: 12716 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.401 AC: 60960 AN: 151886 Hom.: 12745 Cov.: 31 AF XY: 0.396 AC XY: 29406 AN XY: 74244

African (AFR) AF: 0.503 AC: 20816 AN: 41388

American (AMR) AF: 0.317 AC: 4835 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3466

East Asian (EAS) AF: 0.148 AC: 766 AN: 5176

South Asian (SAS) AF: 0.306 AC: 1463 AN: 4788

European-Finnish (FIN) AF: 0.399 AC: 4210 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26061 AN: 67936

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.358 Hom.: 5015

Bravo AF: 0.399

Asia WGS AF: 0.244 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.44
PhyloP100		-0.67

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: rs2051545;

hg19: chr16-13772599;