5-111068487-G-A

Variant names:

• chr5-111068487-G-A
• rs17551370

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 0.129 in 152,012 control chromosomes in the GnomAD database, including 1,379 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 0.13 (1379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19666 AN: 151892 Hom.: 1377 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.141

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.129 AC: 19679 AN: 152012 Hom.: 1379 Cov.: 32 AF XY: 0.130 AC XY: 9685 AN XY: 74296

African (AFR) AF: 0.106 AC: 4395 AN: 41462

American (AMR) AF: 0.0877 AC: 1338 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3468

East Asian (EAS) AF: 0.0622 AC: 322 AN: 5174

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4812

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10572

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10029 AN: 67946

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.134 Hom.: 2423

Bravo AF: 0.116

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs17551370; hg19: chr5-110404185;