rs4431984

chr11-26874358-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 0.391 in 151,586 control chromosomes in the GnomAD database, including 11,850 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 (11850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.391 AC: 59216 AN: 151468 Hom.: 11842 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.391 AC: 59269 AN: 151586 Hom.: 11850 Cov.: 32 AF XY: 0.386 AC XY: 28621 AN XY: 74078

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.397

Alfa AF: 0.382 Hom.: 1780

Bravo AF: 0.386

Asia WGS AF: 0.346 AC: 1202 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.66
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4431984; hg19: chr11-26895905;