rs11799391

Variant names:

• chr1-238136872-A-C
• rs11799391

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 0.0473 in 152,316 control chromosomes in the GnomAD database, including 200 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 0.047 (200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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 (SAS) allele frequency at 95% confidence interval = 0.094 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: 0.0472 AC: 7190 AN: 152198 Hom.: 200 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0892

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0473 AC: 7201 AN: 152316 Hom.: 200 Cov.: 32 AF XY: 0.0469 AC XY: 3492 AN XY: 74484

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0892

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0461 Hom.: 19

Bravo AF: 0.0457

Asia WGS AF: 0.0930 AC: 321 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	3.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11799391; hg19: chr1-238300172; COSMIC: COSV60041971;