16-13806476-A-G

Variant names:

• chr16-13806476-A-G
• rs16962916
• ENST00000761632.1:n.241+1369T>C

Variant summary

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

The ENST00000761632.1(ENSG00000299216):​n.241+1369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 152,192 control chromosomes in the GnomAD database, including 70 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 0.022 (70 hom., cov: 33)
• Consequence: ENSG00000299216 ENST00000761632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 3 publications found

Genes affected

ENSG00000299216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761632.1. 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
	ENSG00000299216	ENST00000761632.1		n.241+1369T>C		intron	N/A
	ENSG00000299216	ENST00000761633.1		n.119+1485T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 3361 AN: 152074 Hom.: 67 Cov.: 33

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00995

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0223 AC: 3387 AN: 152192 Hom.: 70 Cov.: 33 AF XY: 0.0228 AC XY: 1694 AN XY: 74420

African (AFR) AF: 0.0362 AC: 1501 AN: 41482

American (AMR) AF: 0.0235 AC: 359 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3468

East Asian (EAS) AF: 0.0810 AC: 420 AN: 5182

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4826

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10610

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00995 AC: 677 AN: 68018

Other (OTH) AF: 0.0198 AC: 42 AN: 2116

Alfa AF: 0.000119 Hom.: 7000

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.72
PhyloP100		-0.59

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: rs16962916;

hg19: chr16-13900333;