11-4541988-A-G

Position:

• chr11-4541988-A-G

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 0.143 in 152,198 control chromosomes in the GnomAD database, including 1,795 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 0.14 (1795 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4541988A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21787 AN: 152080 Hom.: 1792 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.143 AC: 21820 AN: 152198 Hom.: 1795 Cov.: 33 AF XY: 0.138 AC XY: 10275 AN XY: 74418

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0797

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0681

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.148

Alfa AF: 0.126 Hom.: 2627

Bravo AF: 0.150

Asia WGS AF: 0.115 AC: 402 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	7.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12416860; hg19: chr11-4563218;