rs575030

Variant names:

• chr11-121221689-T-C
• rs575030

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 0.38 in 151,994 control chromosomes in the GnomAD database, including 11,469 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 0.38 (11469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

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 (AFR) allele frequency at 95% confidence interval = 0.477 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: 0.380 AC: 57718 AN: 151878 Hom.: 11460 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.380 AC: 57761 AN: 151994 Hom.: 11469 Cov.: 31 AF XY: 0.381 AC XY: 28282 AN XY: 74292

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.392

Alfa AF: 0.353 Hom.: 2403

Bravo AF: 0.378

Asia WGS AF: 0.362 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs575030; hg19: chr11-121092398;