rs911411

Positions:

• chr20-49101894-C-G
• chr20-49101894-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 0.392 in 151,820 control chromosomes in the GnomAD database, including 11,791 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 0.39 (11791 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 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: 0.393 AC: 59555 AN: 151702 Hom.: 11784 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.392 AC: 59586 AN: 151820 Hom.: 11791 Cov.: 31 AF XY: 0.392 AC XY: 29052 AN XY: 74190

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.413

Alfa AF: 0.398 Hom.: 1482

Bravo AF: 0.389

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs911411; hg19: chr20-47718431;