rs17503512

Variant names:

• chr16-26346113-G-A
• rs17503512
• ENST00000832099.1:n.450-17877G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000832099.1(ENSG00000231876):​n.450-17877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,102 control chromosomes in the GnomAD database, including 10,939 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 0.37 (10939 hom., cov: 32)
• Consequence: ENSG00000231876 ENST00000832099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 3 publications found

Genes affected

ENSG00000231876 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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
ENSG00000231876	ENST00000832099.1	n.450-17877G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56768 AN: 151984 Hom.: 10939 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.373 AC: 56790 AN: 152102 Hom.: 10939 Cov.: 32 AF XY: 0.369 AC XY: 27460 AN XY: 74358

African (AFR) AF: 0.363 AC: 15042 AN: 41476

American (AMR) AF: 0.410 AC: 6260 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3468

East Asian (EAS) AF: 0.173 AC: 897 AN: 5172

South Asian (SAS) AF: 0.274 AC: 1324 AN: 4832

European-Finnish (FIN) AF: 0.345 AC: 3654 AN: 10588

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26749 AN: 67970

Other (OTH) AF: 0.394 AC: 831 AN: 2108

Alfa AF: 0.376 Hom.: 1920

Bravo AF: 0.379

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs17503512; hg19: chr16-26357434;