rs1440714

Variant names:

• chr11-15812277-A-T
• rs1440714

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;