11-5173580-A-G

Position:

• chr11-5173580-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 0.0499 in 152,204 control chromosomes in the GnomAD database, including 537 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 0.050 (537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.0497 AC: 7564 AN: 152086 Hom.: 534 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00588

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0499 AC: 7595 AN: 152204 Hom.: 537 Cov.: 33 AF XY: 0.0477 AC XY: 3552 AN XY: 74428

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00589

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.00533 Hom.: 2

Bravo AF: 0.0551

Asia WGS AF: 0.0170 AC: 59 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128713; hg19: chr11-5194810;