rs1033816

chr6-153947409-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 0.254 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;