chr16-12582672-G-T

Variant names:

• chr16-12582672-G-T
• rs17823157
• ENST00000564505.2:n.347-21526C>A

Variant summary

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

The ENST00000564505.2(ENSG00000259899):​n.347-21526C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,162 control chromosomes in the GnomAD database, including 3,479 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 0.20 (3479 hom., cov: 32)
• Consequence: ENSG00000259899 ENST00000564505.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 9 publications found

Genes affected

ENSG00000259899 (HGNC:58619):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX29-AS3	XR_007064988.1	n.406-14373C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259899	ENST00000564505.2	n.347-21526C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29803 AN: 152044 Hom.: 3483 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.196 AC: 29792 AN: 152162 Hom.: 3479 Cov.: 32 AF XY: 0.194 AC XY: 14393 AN XY: 74376

African (AFR) AF: 0.0881 AC: 3660 AN: 41538

American (AMR) AF: 0.207 AC: 3168 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 886 AN: 3466

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5176

South Asian (SAS) AF: 0.169 AC: 818 AN: 4826

European-Finnish (FIN) AF: 0.194 AC: 2052 AN: 10582

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18188 AN: 67976

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.223 Hom.: 2273

Bravo AF: 0.189

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.33
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs17823157; hg19: chr16-12676529;