rs575030

Variant names:

• chr11-121221689-T-C
• rs575030

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.482 AC: 19991 AN: 41442

American (AMR) AF: 0.302 AC: 4619 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1150 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1489 AN: 5170

South Asian (SAS) AF: 0.466 AC: 2243 AN: 4810

European-Finnish (FIN) AF: 0.402 AC: 4240 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22758 AN: 67966

Other (OTH) AF: 0.392 AC: 828 AN: 2112

Alfa AF: 0.358 Hom.: 4124

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs575030; hg19: chr11-121092398;