16-12582672-G-T

Variant names:

• chr16-12582672-G-T
• rs17823157
• ENST00000564505.1:n.308-21526C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564505.1(ENSG00000259899):​n.308-21526C>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 ENST00000564505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

Genes affected

ENSG00000259899 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
LOC105371085	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	ENST00000564505.1	n.308-21526C>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

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.235

Alfa AF: 0.222 Hom.: 2039

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17823157; hg19: chr16-12676529;