16-59727788-A-G

Variant names:

• chr16-59727788-A-G
• rs965916
• ENST00000565921.4:n.200-17493T>C

Variant summary

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

The ENST00000565921.4(ENSG00000293012):​n.200-17493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,204 control chromosomes in the GnomAD database, including 456 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 0.039 (456 hom., cov: 32)
• Consequence: ENSG00000293012 ENST00000565921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

Genes affected

ENSG00000293012 (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 = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565921.4. 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
	ENSG00000293012	ENST00000565921.4	TSL:3	n.200-17493T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0391 AC: 5953 AN: 152086 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00883

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0392 AC: 5962 AN: 152204 Hom.: 456 Cov.: 32 AF XY: 0.0410 AC XY: 3048 AN XY: 74426

African (AFR) AF: 0.0568 AC: 2357 AN: 41516

American (AMR) AF: 0.0500 AC: 765 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1799 AN: 5146

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4826

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10608

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

European-Non Finnish (NFE) AF: 0.00884 AC: 601 AN: 68022

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0162 Hom.: 41

Bravo AF: 0.0444

Asia WGS AF: 0.151 AC: 522 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.31
PhyloP100		0.21

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: rs965916;

hg19: chr16-59761692;