rs29605

Variant names:

• chr16-8365919-C-T
• rs29605

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.192 AC: 7949 AN: 41454

American (AMR) AF: 0.272 AC: 4152 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1636 AN: 5164

South Asian (SAS) AF: 0.224 AC: 1075 AN: 4806

European-Finnish (FIN) AF: 0.150 AC: 1592 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7480 AN: 67994

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.133 Hom.: 2654

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

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