rs1233335

chr6-29825804-C-Gchr6-29825804-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 0.0469 in 152,294 control chromosomes in the GnomAD database, including 202 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 0.047 (202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7119 AN: 152176 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.00944

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0469 AC: 7139 AN: 152294 Hom.: 202 Cov.: 32 AF XY: 0.0460 AC XY: 3423 AN XY: 74482

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.0548

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.00946

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0124 Hom.: 4

Bravo AF: 0.0536

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1233335; hg19: chr6-29793581;