rs412735

Variant names:

• chr6-33056355-G-A
• rs412735

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 0.408 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.341 AC: 14128 AN: 41482

American (AMR) AF: 0.543 AC: 8299 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1413 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3555 AN: 5178

South Asian (SAS) AF: 0.479 AC: 2305 AN: 4814

European-Finnish (FIN) AF: 0.396 AC: 4182 AN: 10560

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27026 AN: 67968

Other (OTH) AF: 0.396 AC: 838 AN: 2114

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs412735; hg19: chr6-33024132;