16-89675088-A-G

Variant names:

• chr16-89675088-A-G
• rs12443954
• ENST00000615131.2:n.1300+2221A>G

Variant summary

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

The ENST00000615131.2(ENSG00000275734):​n.1300+2221A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,762 control chromosomes in the GnomAD database, including 8,233 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 (8233 hom., cov: 29)
• Consequence: ENSG00000275734 ENST00000615131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 17 publications found

Genes affected

ENSG00000275734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615131.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275734	ENST00000615131.2	TSL:6	n.1300+2221A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47360 AN: 151644 Hom.: 8227 Cov.: 29

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.312 AC: 47390 AN: 151762 Hom.: 8233 Cov.: 29 AF XY: 0.321 AC XY: 23766 AN XY: 74136

African (AFR) AF: 0.342 AC: 14123 AN: 41350

American (AMR) AF: 0.354 AC: 5393 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4035 AN: 5124

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4816

European-Finnish (FIN) AF: 0.333 AC: 3496 AN: 10486

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16847 AN: 67966

Other (OTH) AF: 0.283 AC: 597 AN: 2106

Alfa AF: 0.269 Hom.: 19532

Bravo AF: 0.317

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12443954; hg19: chr16-89741496;