rs1440714

Positions:

• chr11-15812277-A-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 0.406 in 151,752 control chromosomes in the GnomAD database, including 14,504 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 0.41 (14504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

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 (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.406 AC: 61544 AN: 151634 Hom.: 14461 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.406 AC: 61644 AN: 151752 Hom.: 14504 Cov.: 32 AF XY: 0.405 AC XY: 30041 AN XY: 74146

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.372

Alfa AF: 0.367 Hom.: 1412

Bravo AF: 0.434

Asia WGS AF: 0.386 AC: 1328 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440714; hg19: chr11-15833823;