rs1851851

chr11-49931622-T-C

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 0.0411 in 152,262 control chromosomes in the GnomAD database, including 191 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 0.041 (191 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0613 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: 0.0412 AC: 6261 AN: 152144 Hom.: 191 Cov.: 33

Gnomad AFR AF: 0.00989

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0411 AC: 6260 AN: 152262 Hom.: 191 Cov.: 33 AF XY: 0.0403 AC XY: 3002 AN XY: 74432

Gnomad4 AFR AF: 0.00986

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.0538 Hom.: 32

Bravo AF: 0.0375

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.70
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1851851; hg19: chr11-49953174;