11-72548096-G-A

Position:

• chr11-72548096-G-A

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 0.637 in 152,090 control chromosomes in the GnomAD database, including 31,563 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 0.64 (31563 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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: 0.637 AC: 96865 AN: 151972 Hom.: 31554 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.637 AC: 96912 AN: 152090 Hom.: 31563 Cov.: 33 AF XY: 0.638 AC XY: 47444 AN XY: 74344

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.666

Alfa AF: 0.683 Hom.: 57520

Bravo AF: 0.635

Asia WGS AF: 0.699 AC: 2434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs193170; hg19: chr11-72259140;