chr11-15435921-G-A

Variant names:

• chr11-15435921-G-A
• rs7114467

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.220 AC: 9109 AN: 41494

American (AMR) AF: 0.337 AC: 5147 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2938 AN: 5146

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4818

European-Finnish (FIN) AF: 0.486 AC: 5141 AN: 10568

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28983 AN: 67968

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.400 Hom.: 40287

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7114467; hg19: chr11-15457467;