rs29605

Positions:

• chr16-8365919-C-T

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 0.164 in 152,090 control chromosomes in the GnomAD database, including 2,454 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 0.16 (2454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24855 AN: 151972 Hom.: 2459 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.164 AC: 24877 AN: 152090 Hom.: 2454 Cov.: 32 AF XY: 0.171 AC XY: 12726 AN XY: 74352

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.158

Alfa AF: 0.129 Hom.: 1969

Bravo AF: 0.173

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.50
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29605; hg19: chr16-8415921; COSMIC: COSV73889544;