rs7114467

Positions:

• chr11-15435921-G-A
• chr11-15435921-G-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 0.367 in 152,046 control chromosomes in the GnomAD database, including 11,061 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 0.37 (11061 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55797 AN: 151928 Hom.: 11067 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.367 AC: 55790 AN: 152046 Hom.: 11061 Cov.: 32 AF XY: 0.370 AC XY: 27518 AN XY: 74320

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.380

Alfa AF: 0.407 Hom.: 17237

Bravo AF: 0.352

Asia WGS AF: 0.427 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7114467; hg19: chr11-15457467;