rs1033816

Variant names:

• chr6-153947409-C-T
• rs1033816

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 0.254 in 151,638 control chromosomes in the GnomAD database, including 5,119 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 (5119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 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: 0.254 AC: 38531 AN: 151520 Hom.: 5106 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.254 AC: 38550 AN: 151638 Hom.: 5119 Cov.: 32 AF XY: 0.263 AC XY: 19475 AN XY: 74050

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.279

Alfa AF: 0.235 Hom.: 553

Bravo AF: 0.257

Asia WGS AF: 0.386 AC: 1340 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033816; hg19: chr6-154268544;