16-13734612-A-G

Variant names:

• chr16-13734612-A-G
• rs2866845
• ENST00000573369.5:n.702-4176T>C

Variant summary

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

The ENST00000576944.1(ENSG00000262267):​n.384-4176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,078 control chromosomes in the GnomAD database, including 36,890 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 (36890 hom., cov: 32)
• Consequence: ENSG00000262267 ENST00000576944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62
• Publications: 1 publications found

Genes affected

ENSG00000262267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576944.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262267	ENST00000573369.5	TSL:5	n.702-4176T>C		intron	N/A
	ENSG00000262267	ENST00000576944.1	TSL:4	n.384-4176T>C		intron	N/A
	ENSG00000262267	ENST00000659657.1		n.335-4176T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104936 AN: 151960 Hom.: 36886 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.690 AC: 104987 AN: 152078 Hom.: 36890 Cov.: 32 AF XY: 0.694 AC XY: 51614 AN XY: 74330

African (AFR) AF: 0.565 AC: 23447 AN: 41470

American (AMR) AF: 0.649 AC: 9911 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4517 AN: 5172

South Asian (SAS) AF: 0.709 AC: 3412 AN: 4814

European-Finnish (FIN) AF: 0.802 AC: 8479 AN: 10578

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50555 AN: 67980

Other (OTH) AF: 0.674 AC: 1427 AN: 2116

Alfa AF: 0.720 Hom.: 93350

Bravo AF: 0.675

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.94
PhyloP100		2.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2866845; hg19: chr16-13828469;