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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903646	XR_007064997.1	n.234+1369T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299216	ENST00000761632.1	n.241+1369T>C		intron_variant	Intron 1 of 1
ENSG00000299216	ENST00000761633.1	n.119+1485T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs16962916; hg19: chr16-13900333;