rs412735

Positions:

• chr6-33056355-G-A

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 0.408 in 152,076 control chromosomes in the GnomAD database, including 13,280 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 0.41 (13280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.408 AC: 61997 AN: 151958 Hom.: 13259 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.408 AC: 62037 AN: 152076 Hom.: 13280 Cov.: 32 AF XY: 0.412 AC XY: 30604 AN XY: 74330

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.396

Alfa AF: 0.411 Hom.: 1624

Bravo AF: 0.416

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412735; hg19: chr6-33024132;