rs34569362

Variant names:

• chr16-57356149-G-T
• rs34569362

Variant summary

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

The variant allele was found at a frequency of 0.13 in 152,140 control chromosomes in the GnomAD database, including 1,556 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 (1556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19803 AN: 152022 Hom.: 1561 Cov.: 31

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.130 AC: 19790 AN: 152140 Hom.: 1556 Cov.: 31 AF XY: 0.130 AC XY: 9654 AN XY: 74362

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.136

Alfa AF: 0.144 Hom.: 264

Bravo AF: 0.129

Asia WGS AF: 0.212 AC: 735 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	12
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34569362; hg19: chr16-57390061;