chr3-130758722-T-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986023	XR_001740492.2	n.1219-7325A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306101	ENST00000815323.1	n.320-7325A>C		intron_variant	Intron 3 of 4
ENSG00000306101	ENST00000815324.1	n.301-7325A>C		intron_variant	Intron 3 of 3
ENSG00000306101	ENST00000815325.1	n.303-7325A>C		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs16845869; hg19: chr3-130477566;