rs11584383

chr1-200966738-T-Cchr1-200966738-T-G

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 0.234 in 152,268 control chromosomes in the GnomAD database, including 4,548 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 0.23 (4545 hom., cov: 33)
  • Exomes 𝑓: 0.37 (3 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 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: 0.234 AC: 35545 AN: 152112 Hom.: 4540 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.368 AC: 14 AN: 38 Hom.: 3 AF XY: 0.308 AC XY: 8 AN XY: 26

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.444

GnomAD4 genome AF: 0.234 AC: 35559 AN: 152230 Hom.: 4545 Cov.: 33 AF XY: 0.228 AC XY: 16954 AN XY: 74426

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.222

Alfa AF: 0.264 Hom.: 10405

Bravo AF: 0.228

Asia WGS AF: 0.0790 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11584383; hg19: chr1-200935866;