rs3849233

Variant names:

• chr16-87047584-A-G
• rs3849233
• ENST00000836709.1:n.215+8511T>C

Variant summary

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

The ENST00000836709.1(ENSG00000289423):​n.215+8511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,994 control chromosomes in the GnomAD database, including 9,205 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 0.31 (9205 hom., cov: 32)
• Consequence: ENSG00000289423 ENST00000836709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 2 publications found

Genes affected

ENSG00000289423 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289423	ENST00000836709.1	n.215+8511T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47814 AN: 151876 Hom.: 9205 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.315 AC: 47812 AN: 151994 Hom.: 9205 Cov.: 32 AF XY: 0.318 AC XY: 23604 AN XY: 74270

African (AFR) AF: 0.0861 AC: 3575 AN: 41516

American (AMR) AF: 0.335 AC: 5120 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.373 AC: 1912 AN: 5122

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3985 AN: 10548

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28341 AN: 67932

Other (OTH) AF: 0.326 AC: 690 AN: 2114

Alfa AF: 0.368 Hom.: 22250

Bravo AF: 0.293

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs3849233; hg19: chr16-87081190;