rs11587621

Variant names:

• chr1-211495058-T-C
• rs11587621

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 0.276 in 152,104 control chromosomes in the GnomAD database, including 6,043 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 0.28 (6043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.276 AC: 41932 AN: 151986 Hom.: 6041 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.276 AC: 41959 AN: 152104 Hom.: 6043 Cov.: 32 AF XY: 0.271 AC XY: 20127 AN XY: 74360

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.282

Alfa AF: 0.285 Hom.: 1033

Bravo AF: 0.270

Asia WGS AF: 0.199 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11587621; hg19: chr1-211668400;