16-13656867-C-G

Variant names:

• chr16-13656867-C-G
• rs7202384
• ENST00000727119.1:n.213-7616G>C

Variant summary

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

The ENST00000727119.1(ENSG00000294970):​n.213-7616G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,092 control chromosomes in the GnomAD database, including 36,610 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 0.69 (36610 hom., cov: 32)
• Consequence: ENSG00000294970 ENST00000727119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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.213-7616G>C		intron	N/A
	ENSG00000294970	ENST00000727120.1		n.309-7616G>C		intron	N/A
	ENSG00000294970	ENST00000727121.1		n.202-7616G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105104 AN: 151974 Hom.: 36576 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.692 AC: 105188 AN: 152092 Hom.: 36610 Cov.: 32 AF XY: 0.695 AC XY: 51664 AN XY: 74356

African (AFR) AF: 0.607 AC: 25170 AN: 41482

American (AMR) AF: 0.743 AC: 11340 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4395 AN: 5166

South Asian (SAS) AF: 0.783 AC: 3775 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7145 AN: 10590

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48891 AN: 67988

Other (OTH) AF: 0.680 AC: 1435 AN: 2110

Alfa AF: 0.615 Hom.: 1794

Bravo AF: 0.695

Asia WGS AF: 0.796 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-0.33

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: rs7202384;

hg19: chr16-13750724;