rs1533079

Variant names:

• chr16-14377404-G-A
• rs1533079
• ENST00000772675.1:n.283-2886G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-14377404-G-A
• chr16-14377404-G-C
• chr16-14377404-G-T

Variant summary

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

The ENST00000772675.1(ENSG00000300554):​n.283-2886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,166 control chromosomes in the GnomAD database, including 1,803 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 0.13 (1803 hom., cov: 32)
• Consequence: ENSG00000300554 ENST00000772675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

Genes affected

ENSG00000300554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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
ENSG00000300554	ENST00000772675.1	n.283-2886G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20470 AN: 152048 Hom.: 1797 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.135 AC: 20501 AN: 152166 Hom.: 1803 Cov.: 32 AF XY: 0.138 AC XY: 10290 AN XY: 74392

African (AFR) AF: 0.110 AC: 4558 AN: 41508

American (AMR) AF: 0.108 AC: 1643 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 289 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2616 AN: 5164

South Asian (SAS) AF: 0.174 AC: 842 AN: 4828

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8851 AN: 68018

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.125 Hom.: 2515

Bravo AF: 0.132

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.29
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1533079; hg19: chr16-14471261;