rs16845869

Variant names:

• chr3-130758722-T-G
• rs16845869
• ENST00000815323.1:n.320-7325A>C

Variant summary

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

The ENST00000815323.1(ENSG00000306101):​n.320-7325A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 152,250 control chromosomes in the GnomAD database, including 729 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 (729 hom., cov: 32)
• Consequence: ENSG00000306101 ENST00000815323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 4 publications found

Genes affected

ENSG00000306101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815323.1. 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
	ENSG00000306101	ENST00000815323.1		n.320-7325A>C		intron	N/A
	ENSG00000306101	ENST00000815324.1		n.301-7325A>C		intron	N/A
	ENSG00000306101	ENST00000815325.1		n.303-7325A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11613 AN: 152132 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0764 AC: 11638 AN: 152250 Hom.: 729 Cov.: 32 AF XY: 0.0825 AC XY: 6145 AN XY: 74442

African (AFR) AF: 0.0291 AC: 1208 AN: 41558

American (AMR) AF: 0.214 AC: 3277 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0941 AC: 326 AN: 3466

East Asian (EAS) AF: 0.117 AC: 607 AN: 5184

South Asian (SAS) AF: 0.108 AC: 521 AN: 4826

European-Finnish (FIN) AF: 0.0878 AC: 930 AN: 10588

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4538 AN: 68024

Other (OTH) AF: 0.0917 AC: 194 AN: 2116

Alfa AF: 0.0761 Hom.: 1342

Bravo AF: 0.0854

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.38
PhyloP100		1.0

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: rs16845869;

hg19: chr3-130477566;