rs444697

Positions:

• chr6-33607232-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 0.247 in 152,202 control chromosomes in the GnomAD database, including 5,006 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 0.25 (5006 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.247 AC: 37540 AN: 152084 Hom.: 5004 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37551 AN: 152202 Hom.: 5006 Cov.: 33 AF XY: 0.248 AC XY: 18434 AN XY: 74420

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.266

Alfa AF: 0.239 Hom.: 5571

Bravo AF: 0.244

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	16
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: rs444697; hg19: chr6-33575009;