chr16-89674995-G-A

Variant names:

• chr16-89674995-G-A
• rs12918773
• ENST00000615131.2:n.1300+2128G>A

Variant summary

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

The ENST00000615131.2(ENSG00000275734):​n.1300+2128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 151,656 control chromosomes in the GnomAD database, including 530 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 0.076 (530 hom., cov: 29)
• Consequence: ENSG00000275734 ENST00000615131.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 19 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275734	ENST00000615131.2	TSL:6	n.1300+2128G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11552 AN: 151536 Hom.: 529 Cov.: 29

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0762 AC: 11557 AN: 151656 Hom.: 530 Cov.: 29 AF XY: 0.0784 AC XY: 5807 AN XY: 74086

African (AFR) AF: 0.0339 AC: 1402 AN: 41348

American (AMR) AF: 0.111 AC: 1680 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.117 AC: 603 AN: 5146

South Asian (SAS) AF: 0.0783 AC: 375 AN: 4790

European-Finnish (FIN) AF: 0.120 AC: 1264 AN: 10498

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0853 AC: 5793 AN: 67942

Other (OTH) AF: 0.0621 AC: 130 AN: 2092

Alfa AF: 0.0759 Hom.: 529

Bravo AF: 0.0757

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.1
DANN	Benign	0.88
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12918773; hg19: chr16-89741403;