rs29228

Variant names:

• chr6-29655962-G-A
• rs29228

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 0.162 in 152,126 control chromosomes in the GnomAD database, including 2,405 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 (2405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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: 0.162 AC: 24622 AN: 152008 Hom.: 2392 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.162 AC: 24650 AN: 152126 Hom.: 2405 Cov.: 32 AF XY: 0.162 AC XY: 12060 AN XY: 74376

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.162

Alfa AF: 0.188 Hom.: 2182

Bravo AF: 0.157

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	7.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29228; hg19: chr6-29623739;